The original description of Diaptomus vexillifer Brehm, 1933, endemic to Lake Danao (Leyte Island), was elementary and lacking taxonomically satisfactory characters. In this paper, we redescribe the Philippine-endemic genus Filipinodiaptomus Lai, Mamaril Sr. & Fernando, 1979 and the species D. vexillifer collected from its type locality, using light and scanning electron microscopy and an analysis of the mtCOI gene and the ITS of the nuclear 18S operon. We found that D. vexillifer is the second species under this endemic genus. A neotype and paraneotypes are hereby designated. Also a detailed morphological comparison is made between Filipinodiaptomus vexillifer (Brehm, 1933) comb. nov. and Filipinodiaptomus insulanus (Wright, 1928). Their taxonomic characters, interspecies relationship, and biogeography are likewise discussed.