Japanese species of the genus Borophaga are revised. Borophaga clandestina sp. nov. is described, and brief description of a known Japanese species, B. femorata (Meigen), is added. Borophaga clandestina sp. nov. is similar to B. femorata in general appearance, but they are clearly distinguishable in genitalic characters. The aedeagus of Borophaga is a complicated structure composed of multiple sclerites, and completely different from the simple, tube-shaped aedeagus in Stichillus or Peromitra, members of the Stichillus subgroup. The state of the left flattened arm derived from the posterodorsal margin of the hypandrium being broadened at the base could be synapomorphic to the Borophaga subgroup comprising Borophaga, Godavaria, Latiborophaga, Antipodiphora and Abaristophora.