Schindleria is likely the most numerous coral reef associated fish in the world. Yet, we are far from understanding their key to success. Schindleria are tiny (<23 mm) progenetic Gobiidae with a very short generation time. Due to extreme progenesis, its ancestors were morphologically very simple, which resulted in highly similar body constructs across the taxon. Hence, very few distinctive morphologies have been identified, and species descriptions comprise few specimens; for which detailed interspecific differences in body shape and sexual dimorphisms (intraspecific) are still poorly documented. To discriminate between species, especially in sympatry, the most evident feature is the length of the dorsal fin, which has been widely used for the classification into two types: the long dorsal finned (LDF) and short dorsal finned (SDF). In Hawaii, these types are named Schindleria praematura and Schindleria pietschmanni, respectively. We investigated morphometrics of sympatric populations of these two Schindleria from an atoll of the Hawaiian Islands (23° 46′ N, 166° 11′ W) as a first step to assess putative dimorphisms between sexes and between species’ types. Between types, we found significant differences in body size and among features related to propulsion, swimming, and foraging (e.g., the length of the tail or the width of the head), as well as notably different urogenital papillae, which suggests that the two species differ in habitat and in reproductive strategies. Comparing the same sex between the two types, we found that males differed in more morphological traits between the species than females (i.e., 76.2% vs. 52.4%). Within the species, sexual dimorphisms were high in both species (i.e., 71.4% off all traits in S. pietschmanni and 66.7% in S. praematura) and were also linked to swimming (e.g., the length of the dorsal and anal fins and of the tail) and to feeding (e.g., the head length and the snout length), suggesting further intraspecific microhabitat segregation between sexes. We present a rare example of interspecific and sexual morphometric divergence in two sympatric progenetic fishes.