Leontopithecus comprises 4 taxa: black lion tamarins (L. chrysopygus), golden lion tamarins (L. rosalia), black-faced lion tamarins (L. caissara), and golden-headed lion tamarins (L. chrysomelas). Endemic to the Atlantic Forest of Brazil, they are endangered (Appendix I, CITES; IUCN Critically Endangered: Leontopithecus chrysopygus, L. caissara; IUCN Endangered: L. rosalia, L. chrysomelas). The 4 taxa are differentiated morphologically and geographically and occupy different habitat types. However, it is not clear if all of them are separate species, particularly Leontopithecus caissara, or how they are related to one another evolutionarily. Therefore, we investigated lion tamarin differentiation and radiation. We sequenced the mtDNA control region and performed phylogenetic analyses, population aggregation analyses, and Mantel tests for geographic/genetic correlation. Mitochondrial genetic data suggest 3 distinct lion tamarin clades (Leontopithecus chrysomelas; L. caissara; and L. chrysopygus/L. rosalia). Phylogenetic analysis also supports: 1) the basal lion tamarin is Leontopithecus chrysomelas, and not L. chrysopygus, 2) L. caissara is not subspecific to L. chrysopygus, and 3) Quaternary forest refugia may have shaped lion tamarin diversification via a pattern that does not follow the theory of metachromism. Even though mitochondrial genetic analyses do not unequivocally support the 4 lion tamarins as separate species, one should consider the 4 lion tamarins, with equal conservation priority based on the combination of morphological, genetic, and habitat differentiation. Each of them is an extremely valuable flagship species that focuses attention on the diminishing, highly endemic Atlantic Forest of Brazil.