An updated checklist of freshwater fishes occurring in the Philippines is presented, with notes on their distribution and conservation status. Information was systematically and comprehensively reviewed, and compiled from current and historical sources including published literature, institutional reports, museum records, and online databases. Results indicate a total of 374 fish species within 29 orders and 78 families to occur in the country. Two hundred and twenty-five (60.16%) species are native, of which 85 (22.73%) are endemic; and an additional 64 (17.11%) are non-native. Gobiiformes is the most diverse order (114 species, 5 families), followed by Cypriniformes (54 species, 4 families) and Perciformes (28 species, 13 families). The most speciose family is Gobiidae (89 species), which represents 23.80% of the total fish diversity. Conservation status based on the IUCN Red List indicates that 57 (15.24%) fish species are assessed as “Data Deficient”, 188 (50.27%) are “Least Concern”, nine (2.41%) are “Near Threatened”, 22 (5.88%) are “Vulnerable”, 20 (5.35%) are “Endangered”, 10 (2.67%) are “Critically Endangered”, 15 (4.01%) are “Extinct”, and the conservation status of a further 53 (14.17%) have not been assessed (Not Evaluated). The relatively high number of ‘Data Deficient’ species emphasizes the lack of information on the taxonomy, distribution, life history and population status of many species in the archipelago. Detailed studies on various aspects of the biology and threats is highly recommended to advance the scientific understanding of, and develop conservation plans for the freshwater fish species of Philippines.