To assess the accuracy of species delimitation in the genus Aphaenomurus Yosii, we conducted a comparative micro-morphological study and molecular analysis using two mitochondrial (COI, 16S) and two nuclear genes (18S, 28S) on 118 specimens from 24 localities. The results showed that the morphological characters of A. vicinus and A. interpositus, as presented in the original description, were intermixed in phylogenetic lineages within the genus and did not form independent lineages. Furthermore, there were enough differences among Aphaenomurus individuals to be considered as morphologically distinct species (Th. III is 1+1 or 2+2, Abd. I is 2+2 or 3+3, Abd. II is 2+2 or 3+3), but they do not form an independent lineage. Molecular and morphological analyses have determined that A. vicinus and A. interpositus are the same species, exhibiting morphological variation in dental spines formula, claws, chaetotaxy, and other features. Additionally, the genus Aphaenomurus forms a monophyletic clade, which is further divided into several lineages within the genus. No morphological differences were observed to distinguish these lineages. This cladistic divergence is attributed to heteroplasmy, which is supported by previous studies that have suggested the possibility and problems of heteroplasmy in Collembola, and by the high genetic distances between individuals in the mitochondrial genes of Aphaenomurus.