Nineteen species and subspecies of freshwater crabs from the anomuran family Aeglidae are represented in Chile, 16 of which are endemic to this country. We sequenced ∼2,600 nucleotides of the 12S, 16S, COI, and COII genes from mitochondrial DNA to estimate phylogenetic relationships among the Chilean aeglids. We sampled 16 putative Chilean species and subspecies and one morphologically unrecognized taxon according to the most recent Aeglidae classification. In addition to the Chilean aeglids, one sample of Aegla riolimayana and two samples of Aegla affinis were collected from Argentina to check previous hypotheses about the origin of the group. Two other anomurans, one galatheid (Munida subrugosa) and one porcellanid (Pachycheles haigae), were sequenced to serve as outgroups in our phylogenetic analysis. Our results show the clear separation of Aegla papudo from the other Aegla species, as has been suggested previously based on morphology. Its basal position in the Aeglidae trees also supports a Pacific origin for the Aeglidae. Our phylogenies provide strong monophyletic support for the currently recognized species, with the exception of Aegla laevis and Aegla cholchol samples, which form nonmonophyletic groups.