Cryptic species are a biological phenomenon only recently recognized due to progress in molecular studies. They pose a significant challenge to conventional taxonomic work since these species manifest low morphological differences, but considerable genetic disparity. New taxonomic methods are in development but have yet to be tested for many animal groups. Isopods belonging to the suborder Microcerberidea are one such group. The Asian microcerberid isopod, Coxicerberus fukudai (Ito, 1974), is a major component of marine interstitial fauna with suspected cryptic species inhabiting Japan and Korea. We chose six Korean populations with high molecular interpopulations divergence and applied 2D landmark-based geometric morphometrics to cephalic sensilla, pleonal points, and male pleopod II. This quantitative approach allowed us to study interpopulation size and shape variations, morphospace structure, and whether the morphological pattern mirrored the genetic species. We determined that a high degree of interpopulation size variation significantly influences shape changes. Once we removed the allometric effect, the size-corrected male pleopod II shape variations yielded a new species, C. jangsaensis sp. nov. At the same time, we were able to resolve the C. fukadai species complex.