Representatives of species of alpheid shrimps included in Synalpheus Spence Bate, 1888 exhibit spectacular and distinct behaviors such as eusociality. The wide range of morphological variations in these taxa makes taxonomic understanding difficult. The phylogenetic relationships of the species that comprise the Synalpheus brevicarpus (Herrick, 1891) complex are little known, especially for individuals from South America. Our investigation represents an additional approach to elucidate some aspects of the phylogeny of this species complex. Morphological and molecular evidence resulting from our analyses revealed the existence of a cryptic entity within the S. brevicarpus complex in southeastern Brazil.