Among the eight genera of Eleotridae known from the Neotropics, two, Microphilypnus and Leptophilypnus, are greatly reduced in size and, along with the Australian genus Philypnodon, form a separate phylogenetic radiation from the other six genera. Microeleotris was described with Leptophilypnus, but Hildebrand later placed the two in synonymy. The original descriptions for these taxa were brief and did not include illustrations. As a result, confusion exists, particularly with regard to the identity of the three described species of Microphilypnus: M. ternetzi, M. amazonicus, and M. macrostoma. Three valid species of Leptophilypnus are known: L. fluviatilis, L. panamensis, and a new species from the Gulf of Mexico drainages of Guatemala that is described herein. Microphilypnus is diagnosed and new information is offered on types of the three nominal species and the habitat characteristics of the genus.