Mindanao has a long, complex and remarkably colorful history. To settlers, it is a Promised Land (Lupang Pangako) rich in natural resources. Much of the region's history circles on a long, ongoing ethno-religious conflict between Christian migrants and native Muslims; religious clashes have been going on since the arrival of the Spaniards on the island in the late 1500s.

Until the late 19th century, almost the entire northern coast of Borneo and parts of the Philippines — more-or-less everything from Sarawak to Mindanao — was heavily infested with pirates, and most of the area was ruled by pirate kings. The Sultanate of Sulu ruled all of the Sulu Islands and Palawan plus parts of Borneo and mainland Mindanao, and its capital Jolo (on Sulu) had a great slave market. The Spanish, the British, the Sultan of Brunei, the White Rajas of Sarawak, and later the Americans fought wars against the pirate kingdoms and eventually shut them down, but it was quite a struggle.

Pirates from Mindanao often raided towns in other parts of the Philippines. Towns like Altavas and Bolinao were built inland to avoid them, while others had fortifications or a warning system like the Dumaguete bell tower. This may not be entirely ended; in 2001 a group based in Basilan grabbed 20 hostages near Puerto Princesa in Palawan and in 2015 another bunch grabbed four near Davao. In both cases the raiders arrived by boat and some hostages were eventually murdered.

The Moros vigorously resisted Spanish, American and Japanese rule for several reasons: Moro nationalism, anti-colonialism, Islam, and piracy. Today some are still resisting the Philippine government. The Autonomous Region in Muslim Mindanao (ARMM) was established in 1989 to give them partial independence, and a peace deal between the government and the largest Moro militia group (Moro Islamic Liberation Front or MILF) was signed in 2012. However there are still armed rebel groups in some areas and a substantial Philippine military presence to suppress them; the two sides reportedly have ties to Al Qaeda and the CIA respectively. On January 2019, ARMM was replaced by the Bangsamoro region after a successful plebiscite.

Moros still talk about a battle at Bud Dajo on Sulu in 1906 where, according to Moro accounts and American critics of the war such as Mark Twain, American forces massacred almost 1000 people, mostly women and children. Some draw parallels with current events; naval guns were used at Bud Dajo to kill at a distance, much as drones are used today. In official American accounts it was a justified counter-insurgency action with some collateral damage, many of the women were armed and some of the children were being used as human shields.

Mindanao occupies about 98,000 km² (38,000 sq mi), or about 33% of the Philippines' territorial area, making it larger than countries such as the Netherlands, South Korea, and Austria, to mention a few.

Mindanao has a great variety of terrain, having ten mountain ranges, two plateau areas, and many swampy lowlands. Most of the island has scattered mountain ranges, but the central and eastern parts has the most mountains, and sprawling plains between them, especially in the Soccsksargen region.

Most of Mindanao is covered with rainforest and some peat swamps, but they have been mostly cleared out for farmland and a few oil palm plantations.

Off the southwest end of Mindanao are the Sulu Islands, a chain leading almost all the way to Sabah, which is the easternmost province of Malaysia, located on the island of Borneo.

Mindanao's population is diverse, even before colonial times. With a population of over 28,000,000 (2015 figures: over 22% of the Philippines' total), it is the second most populous island of the Philippines and the eighth in the world.

Most of Mindanao's non-indigenous people are of Visayan, and occasionally Ilocano and Tagalog heritage, mostly migrants brought by American-era resettlement programs in the 1930s. They form over 50-60% of the population.

The southwestern portion of Mindanao, from the Sulu Archipelago to Maguindanao and the Lanao provinces, is the homeland of the Moro (Filipino Muslim) people, which are rather a grouping of ethnic groups which practiced Islam long before the Spaniards arrived.

A predominantly Muslim group, the Sama-Bajau (Badjao, also "Sea Gypsies"), live mostly on boats and are found in the Philippines, Malaysia and Indonesia. There has always been extensive trade between Mindanao and Borneo, and the Badjao do much of that trading. They are also found in most other parts of the Philippines, and often seen as beggars or vagrants in the cities.

The rest of Mindanao, especially the forested interior, are the ancestral lands of the animist Lumad, rather an umbrella term for all the non-Muslim indigenous peoples of Mindanao. They used to live in most of Mindanao not inhabited by the Moros, until Christian immigrants, primarily Visayans and Ilocanos under American-era resettlement drove them into the mountains. The Lumad are facing an uncertain future, having been repeatedly accused of harboring communist rebels, but they are striving to keep their culture and lifestyle alive.

Being 10 degrees north of the equator, most of Mindanao have a tropical climate, with just two seasons, though it really rains at any time for each season. In reality though, the climate is far from uniform, with the northern and eastern parts of the island which faces the Pacific generally wet all year, and the southern and western parts mostly hot and dry.

Mindanao can be said to be outside the typhoon belt, but it can be struck by typhoons during the final months of the year.

Francisco Bangoy International Airport in Davao City (DVO ^IATA) is the main port of entry by plane, and there are international flights from Singapore (on Scoot), Doha (on Qatar Airways), Quanzhou (on XiamenAir), and Manado (on Garuda Indonesia). Laguindingan Airport (CGY ^IATA) is the second most important airport, but only receives domestic flights and has a short runway which cannot accommodate larger aircraft.

The other airports with regular flights are:

• Zamboanga City (ZAM ^IATA) - Cebu Pacific and Philippine Airlines from Manila and Cebu, PAL Express from Kota Kinabalu (suspended).
• Dipolog (DPL ^IATA) - Cebu Pacific and PAL Express from Manila, and Cebgo from Cebu
• Pagadian (PAG ^IATA) - Cebu Pacific and PAL Express from Manila and Cebgo from Cebu.
• Ozamiz (OZC ^IATA) - Cebu Pacific from Manila and Cebu, and PAL Express from Manila
• Cotabato City (CBO ^IATA) - Cebu Pacific from Manila and Cebu, Philippine Airlines from Manila
• General Santos (GES ^IATA) - Cebu Pacific from Cebu, Iloilo and Manila. Philippine Airlines from Manila, Cebu, and Iloilo
• Camiguin (CGM ^IATA) - Cebu Pacific and PAL Express from Cebu, SkyJet from Manila
• Butuan (BXU ^IATA) - Cebu Pacific and PAL Express from Manila and Cebu
• Surigao City (SUG ^IATA) - Cebu Pacific from Manila and Cebu
• Siargao (IAO ^IATA) - Cebu Pacific from Manila and Cebu, PAL Express from Clark and Cebu.

Zamboanga, Pagadian, Dipolog, Cotabato and Butuan can accommodate flights using medium-sized jet aircraft like Airbus A320s or Boeing 737s, but the others are only capable of accommodating turboprop planes and small business jets. General Santos, meanwhile, can accommodate large jets such as the Airbus A330 and Boeing 777 in addition to smaller jets and turboprop planes.

Ferries connect Mindanao with Luzon and Visayas, and internationally from Malaysia (Sandakan) and Indonesia (Bitung).

• Ferries from Cagayan de Oro connect with Manila, Iloilo, Bacolod, Cebu City, and Tagbilaran .
• Zamboanga City is connected by ferry to Manila (via Dumaguete), and Sandakan in Malaysia.
• Lipata port in Surigao City is served by roll-on/roll-off (RORO) ferries link from Leyte, and ferries from Cebu.
• Nasipit in Butuan has ferries from Manila, Iloilo, Bacolod, Cebu, and Jagna.
• Dapitan is served by RORO ferries from Dumaguete on companies such as Aleson, Montenegro, and Super Shuttle.
• Dipolog has ferries from Manila, Iloilo, Bacolod, Cebu.
• The other ports in Iligan, Ozamiz, and Dipolog is connected to Manila, Iloilo, Bacolod, and Cebu.

Philtranco has deluxe buses to Davao, Cagayan de Oro, Butuan, Tandag, Bislig, Tagum and Surigao going to/from Manila via Lucena, Naga, Iriga, Legazpi, Calbayog and Tacloban. Since 2022, Davao Metro Shuttle also runs a Manila–Davao service, with luxury Volvo buses.

PP Bus Lines also has a similar daily service from Manila to Davao City, but with non-air-conditioned vehicles.

Ceres Liner, the largest bus company in the Visayas, operates a Dumaguete to Dipolog service, which takes the ferry to Dapitan. Bachelor Express also has buses from Tagbilaran and Tubigon in Bohol and Ormoc and Tacloban in Leyte to Davao and Butuan.

Mindanao's long-haul bus services are dominated by the Bacolod-based company Yanson Group of Bus Companies, which runs services through its three subsidiaries in the island:

• Bachelor Express. Largest bus company in the eastern Mindanao area, it operates most routes in Caraga and Davao regions from its Butuan and Davao City bases, as well as services along the Butuan-Cagayan de Oro corridor. Bachelor Express buses are painted a vivid yellow; its luxury buses are branded Bachelor Tours. (updated Sep 2020)
• Mindanao Star. Runs from Davao City to Cotabato City, Davao City to Koronadal via Kidapawan or General Santos, Davao City to General Santos, and Davao City to Samal Island. Buses are painted white, with company logos and markings, and almost all services are run by air-conditioned luxury coaches. (updated Sep 2020)
• Rural Transit. Serves most of northern, central and western Mindanao, with routes from its Cagayan de Oro and Pagadian bases to most of Northern Mindanao, Zamboanga Peninsula, Koronadal, Davao City, and Cotabato City, as well as from Zamboanga City to major destinations within Zamboanga Peninsula. Buses are painted red; its air-conditioned luxury buses are branded Rural Tours. (updated Sep 2020)

Other major bus companies are:

• Davao Metro Shuttle (DMS). Based in Davao City, they operate medium-distance services between the major cities in Davao region. Despite its name, they also operate routes in Caraga, and Arakan in North Cotabato, and also has buses to Leyte and Manila which take the ferry. DMS's fleet are a mix of minibuses and full-size buses, with minibuses used in some short routes and some services plying Davao-Tagum. (updated Sep 2020)
• Super Five. Runs from CDO to Balingoan, Iligan and Valencia (updated Sep 2020)
• Yellow Bus Line (YBL). The oldest bus company in Mindanao, it has services between Koronadal and Tacurong, Isulan, General Santos, and Davao City via GenSan and Digos. (updated Sep 2020)

Most cities and towns in Mindanao have one centralized bus station, generally near downtown. The hub cities, Davao, General Santos and Cagayan de Oro, have one central terminal providing easy transfers between bus lines, though Cagayan de Oro is an exception, with two separate terminals, which means you have to take local public transport to reach the other terminal. For example, if transferring from a bus coming from anywhere in western Mindanao to a bus headed for Davao, you must take a jeepney or a taxi to the terminal for trips to eastern Mindanao.

Traveling by bus through Mindanao can be dangerous, especially in Northern Mindanao, Zamboanga, and Bangsamoro. There have been cases of terrorist groups planting bombs on buses, and passengers can get robbed by bandits. Due to those, buses in Mindanao may only stop at designated stops and stations, and luggage are inspected by transportation police before being placed onto the cargo compartment.

Flying is a possible alternative to the slower provincial buses for long distances in Mindanao, and are the only other way to get between the mainland and Sulu Archipelago beside the ferries.

Cebu Pacific and Cebgo flies to Cagayan de Oro and Zamboanga City from their Davao hub and to Tawi-tawi from Zamboanga, while PAL Express flies to Zamboanga and Siargao from Davao and to Tawi-tawi from Zamboanga City and Cotabato City. Bangsamoro Airways flies to the Sulu islands from Cotabato City using smaller commuter aircraft.

Driving is not a good option due to the relative high accident rate, the risk of being attacked and robbed by bandits around Bangsamoro, and the lack of rental agencies outside the largest cities, but is an enjoyable experience as open roads are more possible here and some inland locations are only best reachable by car or motorcycle.

Mindanao proper has a good network of national highways, linking most major cities with each other. Traffic is relatively light, with less cars but more motorcycles, tricycles, and larger and longer trucks. Most cities and towns only grew during the American era, with more centralized settlements surrounded by large swaths of rural land, and roads are quite wider as there are a few houses built close to the road. Road quality has been improved through efforts to widen the most travelled highways, but this is only true for most of the mainland (except Bangsamoro or the former ARMM).

Car rental is only available on the largest cities (e.g. Davao), and if you intend to drive a lot, you could either bring a vehicle from Luzon or buy one within the island (useful if you intend to stay in Mindanao for the long term).

Small tourist towns and the outlying islands (e.g. Siargao, Camiguin) have motorcycle rentals, but is only good for trips within a few kilometers from town.

Ferries and boats connect mainland Mindanao with outlying islands. There are also a few services between coastal cities in the mainland, but are slower than a bus ride or a flight.