We constructed a phylogenetic hypothesis of the pattern of colonization of Philippine scops owls (Otus and Mimizuku). Two mitochondrial genes, ND2 and cytochrome b, were sequenced for 12 samples representing six Philippine endemic taxa: three endemic species, one of which has three endemic subspecies; and one endemic genus. Topology, branch length information, and sequence divergence were used to present the hypothesis for the pattern, direction, and sequence of island colonization events. Philippine scops owls are in two well-supported clades, consistent with at least two independent colonization routes. One route is represented by the montane clade of Otus sunia, O. longicornis, and O. mirus. The other clade is represented by three subspecies of the lowland O. megalotis. The basal position of Mimizuku gurneyi relative to the megalotis clade suggests early colonization of Mindanao. Branch lengths and sequence divergence data are congruent with the morphological differences among the megalotis races. The three races of megalotis differed in 15 of 16 morphological characters. Based on molecular and morphological evidence, we recognize the following Otus megalotis subspecies as full species: Luzon Lowland Scops Owl (O. megalotis), Mindanao Lowland Scops Owl (O. everetti), and Visayan Lowland Scops Owl (O. nigrorum). We also propose reassigning the Giant Scops Owl (Mimizuku gurneyi) to the genus Otus for phyletic consistency.