Cryptic species are a major challenge for morphologically based species identification. Molecular approaches to species delimitation can be a valuable tool to provide preliminary taxonomic hypotheses and significantly complements morphological taxonomy. In South America, the freshwater crabs of the genus Aegla have sparked much interest as they are key species in the often‐endangered freshwater ecosystems and themselves are often considered endangered species. Morphological similarity among Aegla species is not always positively correlated with genetic relatedness and growing evidence suggests that several putative single taxa are actually assemblages of cryptic species. We coupled broad geographically sampling (Argentina, Brazil and Uruguay) with multilocus (COI, 16S and ANT) phylogenies to investigate the diversity of Aegla uruguayana. Our species delimitation analyses suggested that 19 aeglid populations form a well‐supported clade, although individuals from 10 populations possibly represent a complex of cryptic species. The significant amount of cryptic diversity found in aeglids seem to rely on several factors, including habitat fragmentation, life history features, morphological stasis, convergent evolution and recent divergence. The search for new diagnostic characters and the description of the cryptic species that remain unnamed will probably be the next challenge for this unique group of crustaceans.
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