Diatoms from Palawan, a Philippine island separating the Sulu and South China Seas were studied. Samples were collected from freshwaters running over limestones, shists and heavy-metal rich rocks; a lake; aerial habitats; marine littoral and marine benthic habitats. Of the freshwater habitats, streamside pools within rainforest and epiphytic communities in a calcareous lake were the richest in taxa. The surfaces of sand, submerged angiosperm leaves and macroalgae were the richest marine habitats. A total of 348 species, varieties and forms in 74 genera were found, the majority of which were new Philippine records. Navicula was represented by 51 taxa, Mastogloia by 39, Amphora by 22 and Nitzschia by 22. Amphora subhyalina Podzorski & Hakansson, Amphora staurohyalina Podzorski & Hakansson and Anomoeoneis irawanae Podzorski & Hakansson are described as new species.