The marine interstitial Microloxoconcha dimorpha n. sp. has two morphotypes in the male, “L type” and “S type”; they occur sympatrically and can be distinguished by the size of their carapaces and the morphology of the male copulatory organs. Conversely, the genetic relationships based on the partial mitochondrial COI gene did not demonstrate an independent clade as belonging to only one type. The L and S types are therefore not reproductively isolated from each other, and they express an intra-sexual dimorphism. We also argue that the morphological features of the male copulatory organ could have changed prior to the establishment of reproductive isolation.