We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of CentralAmerican cichlid ﬁshes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanningthe geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade,with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama.Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-speciestaxonomy as a result of species-level polyphyly. Bayes factor comparisons of species delimitation modelsaccounting for incomplete lineage sorting under the multispecies coalescent decisively supported the recognitionof two distinct species within Amatitlania corresponding to Amatitlania nigrofasciata and A. kanna lineages. Theonly clearly genetically and morphologically diagnosable species was A. kanna. These results strongly suggestthat incomplete lineage sorting provides the best explanation for the polyphyly of A. kanna, whereas thepolyphyly of A. siquia is likely a result of an imperfect taxonomy. Additional insights from coalescent-dating,network, and historical demographic analyses suggested that the two species of Amatitlania diversiﬁed only sincethe early Pleistocene, and that A. nigrofasciata experienced population expansions from approximately 200 000years ago in the mid-late Pleistocene onward. We discuss implications of our results for the taxonomy andevolutionary history of Amatitlania and, more broadly, of Central American freshwater ﬁshes.