[2] Due to differences in plummage, It is recognized by the International Union for Conservation of Nature as two distinct species with the birds from Basilan and Mindanao classified as the South Philippine dwarf kingfisher and the North Philippine dwarf kingfisher for the rest of its range.

[3][2] The Philippine kingfisher was formally described by the German naturalist Johann Jakob Kaup in 1848 under the binomial name Alcedo melanura.

[6] The Philippine dwarf kingfisher is now placed in the genus Ceyx that was introduced by the French naturalist Bernard Germain de Lacépède in 1799.

[7][8] Three subspecies are recognised:[8] The subspecies C. m. mindanensis is sometimes treated as a separate species, the south Philippine dwarf kingfisher (Ceyx mindanensis), with the nominate and samarensis classified by the Handbook of the Birds of the World as the north Philippine dwarf kingfisher.

[9] The two proposed species are differentiated by color and size: north Philippine dwarf kingfishers have dark blue spotted wings and ears and are slightly smaller than south Philippine dwarf kingfishers, which have a more noticeable lilac hue and are overall more uniform orange.

The IUCN Red List follows the Handbook of the Birds of the World thus assesses the North and South subspecies separately.