Abstract Atya gabonensis Giebel, 1875 and Atya scabra (Leach, 1816) are amphidromous shrimps. In some areas, these species populations are vulnerable due to the anthropogenic impact on their habitats and commercial exploitation. However, basic morphometric data is still lacking. This study provides morphometric data on both species in the Fluvial Island Domain of Paraíba do Sul River basin, Brazil. Sampling was performed bimonthly from January 2013 to March 2014. Individuals were analysed according to sex, weight, carapace length and width, abdomen length, second abdominal pleura height and width, length of third pereopod articles, and length and width of the male appendix interna. We sampled 42 individuals of A. gabonensis and 16 individuals of A. scabra. In both species, females showed abdomen and second abdominal pleura larger than males, while males showed third pereopod articles larger than females, both related to sexual dimorphism. We detected differences in the carapace length × carapace width relationship and in the growth pattern of the male appendix interna between species, with A. gabonensis presenting the carapace and the male appendix interna wider than A. scabra. Morphometric aspects of both species are unpublished for this region, and this data is valuable for A. gabonensis in the western Atlantic and for A. scabra from Rio de Janeiro state. Such information is essential for future systematic assessment and establishment of conservation management policies.