Kota Kinabalu or Puerto Princesa?

Kota Kinabalu has the easier and better swimming. Manukan, Sapi and Mamutik in Tunku Abdul Rahman Park are a short speedboat ride from the central jetty, with coral just off the sand. The resorts at Tanjung Aru and Dalit Bay let you stay with the sea right in front of you. The catch is that the island beaches are small and fill up by late morning.

Puerto Princesa looks out on mangroves and mud, so a swim always means a trip out. The options are the sandbars of Honda Bay, the long, empty sand of Nagtabon or the beach at Sabang. Many people who come for the beach end up moving north to El Nido.

Kota Kinabalu gives you much more to eat. You can pick your crab and lobster from the tanks, try charcoal-grilled stingray at the night market, and eat sang nyuk mee and Tuaran mee in kopitiams that cook dishes you will not find elsewhere.

Puerto Princesa has a shorter list of good things: baywalk grills, chao long left by the Vietnamese refugee community, and raw tamilok for the curious. Both cities cure raw fish in a sour dressing, hinava in Sabah and kinilaw in Palawan, but only Kota Kinabalu has enough depth to make food a reason to go.

Neither city has much to see, and either can be covered in a morning or an afternoon. What differs is the story each tells. Kota Kinabalu's sights look at Borneo's peoples, through the Sabah Museum's longhouse village and the two big mosques. Puerto Princesa's centre on its blue Gothic cathedral and the wartime ruins of Plaza Cuartel, with the open prison farm at Iwahig as an odd extra.

Kota Kinabalu has a little more going on after dark. Its waterfront bars face the sunset over the islands, and a few live-band bars and small clubs stay open late at weekends. Puerto Princesa's evenings are a stroll along the baywalk and a drink on Rizal Avenue. The town is quiet before midnight and has no clubs at all.

Both are nature destinations first, but Kota Kinabalu covers more ground. You can climb Mount Kinabalu through cloud forest full of orchids and pitcher plants, raft the Kiulu and Padas rivers, dive in the marine park and look for proboscis monkeys on the Klias wetlands.

Puerto Princesa's centrepiece is one remarkable sight. The Underground River is paddled by boat through limestone caves in jungle-covered karst. Add the Honda Bay reefs, morning dolphin trips and Ugong Rock, and you have a strong few days rather than a wide range.

Kota Kinabalu has a few places worth a day out. The Sunday tamu at Kota Belud brings Bajau and Dusun villagers together to trade, the 1890s railway rattles south through rice fields to Papar and Beaufort, and Kundasang has its death march memorial.

From Puerto Princesa, nearly every outing is to a river, reef or island, and the villages along the way are not reasons to go. Towns worth seeing in Palawan are too far for a return trip, so you have to move on to reach them.

Kota Kinabalu is the easier choice with children. The islands are short boat rides away with calm shallows. Lok Kawi has orangutans, pygmy elephants and a petting area, and the big resorts have kids' clubs. The drawbacks are poor pavements and long drives to the mountain.

Puerto Princesa's outings do appeal to children: the cave boat ride, the Honda Bay sandbars, the crocodiles and the firefly canoes. But getting to them means early starts, long van rides to Sabang and tricycles with no room for a car seat.

Getting around is awkward in both cities, and neither has public transport a visitor can rely on. In Kota Kinabalu you can walk the waterfront strip between Gaya Street, the markets and the island jetty, and cheap ride-hailing covers the rest. In Puerto Princesa you hop on tricycles around a small, hot centre close to the airport. Every trip out of town is by tour van or hired driver.

Kota Kinabalu has more worth browsing. On Sundays Gaya Street fills with orchids, rattan and batik. The waterfront handicraft market sells pearls and weaving from Sabah and the southern Philippines, and the big malls cover the international chains. Puerto Princesa's shopping is mostly pasalubong: cashews, dried fish, pearls of uneven quality and grass mats from souvenir shops along the main roads.

The two are equally cheap day to day, and in both the money goes on the outings rather than on meals, rides or rooms. In Kota Kinabalu the big costs are the Mount Kinabalu permits, compulsory guides and the mountain hut, along with diving, rafting and the beachfront resorts. In Puerto Princesa they are the Underground River tours, boat hire and environmental fees, while the town guesthouses stay very cheap.

Neither city has a theatre or concert programme, and on most nights live music means cover bands in bars. Kota Kinabalu has one real exception. At the Kaamatan harvest festival in Penampang, gong ensembles and bamboo bands play for local people, not for tourists. In Puerto Princesa the cultural dance shows are put on mainly for tour groups.

For relaxing, the two are much the same: cheap massage all over town, resort spas and an unhurried pace, with no bathing tradition in either. Kota Kinabalu adds the open-air sulphur tubs at Poring Hot Springs, a good soak after the climb. Puerto Princesa offers hilot, the traditional Filipino healing massage, which is welcome after its long van rides.