Abstract Two new species of freshwater anomurans, Aegla pomerana and Aegla muelleri (Decapoda: Anomura: Aeglidae), are described from the Itajai River basin, the major basin of the Atlantic range, located in the northeastern part of the state of Santa Catarina, Brazil. The new taxa can be distinguished from their congeners based on both morphological and molecular evidence (the nuclear gene 28S, and the mitochondrial genes 12S, 16S, COI, and COII). Based on molecular data, A. pomerana has a phylogenetic relationship with A. leptodactyla, but morphologically these two species differ in several characters. Aegla muelleri is a member of the same clade as A. leptochela, but several morphological characters distinguish the two species. New records of occurrence of A. jarai and A. odebrechtii, which occur in the same hydrographic basin, are provided.