Penopus microphthalmus differs from P. japonicus by the following characters: has a higher number of dorsal, 135-158 (vs. 117) and anal, 106-122 (vs. 89) fin rays; lower number of preopercular spines, 4-7 (vs. 9); indistinct spine behind the posterior nostril (vs. distinct, 1% SL); by the bigger horizontal diameter of the eye 1.1-1.6% SL (vs. 0.8); and in having an almost fully scaled head (vs. squamation of the head restricted to the middle part of the preopercle) (Ref. 87601).