We investigated the phylogenetic relationship and differences in the song structure between the Philippine Bush Warbler (Cettia seebohmi) and the Japanese Bush Warbler (C. diphone). We compared complete sequences of the mitochondrial cyt-b gene of C. seebohmi to those of other Cettia taxa from GenBank and found C. seebohmi formed a monophyletic group with C. haddeni and C. diphone. The phylogenetic tree also suggests that C. seebohmi is more closely related to C. haddeni than to C. diphone although this was not strongly supported due to the low bootstrap values. The estimated nucleotide differences between C. seebohmi and C. haddeni (4.37%), and between C. seebohmi and C. diphone (3.87–4.37%) were larger than the inter-subspecific difference between C. diphone borealis and C. d. cantans (2.44%). Cettia seebohmi, C. haddeni, and C. diphone diverged prior to the subspecies divergences of C. diphone. The basic structure of songs was similar in C. seebohmi and C. diphone; all songs consisted of pure monotone whistles followed by variably modulated warbles. However, sonagraphic parameters showed statistically significant differences between species. It is reasonable to regard C. seebohmi and C. diphone as separate species.