The diurnal, brightly colored, and toxic frogs of the genus Mantella are among the most prominent representatives of the endemic anuran fauna of Madagascar. Especially three closely related species, M. aurantiaca, M. crocea, and M. milotympanum, are intensively collected for the pet trade, although basic data on their natural history and genetic diversity are still lacking. Our phylogenetic analyses based on 2.8 kbp of partial 16S rRNA, 12S rRNA, cytochrome b, and rhodopsin DNA sequences confirmed that these species belong to one of the five major clades in Mantella, the M. madagascariensis group. A haplotype network constructed using 830 bp of cytochrome b in 49 individuals from seven populations revealed that M. milotympanum and M. crocea have largely similar haplotypes sharing, confirming doubts about the species validity of M. milotympanum and indicating independent evolution of bright orange pattern in M. milotympanum and M. aurantiaca. Further, clustering of four individuals of M. aurantiaca from Andranomena with M. crocea suggests incomplete lineage sorting or introgression resulting from secondary contact of refugial populations. AMOVA confirmed significant intrapopulation nucleotide diversity (>20%). These diversity patterns and our field observations indicate relatively large population sizes. Hence, overcollecting is probably a minor problem and conservation efforts should rather focus on saving some large populations from habitat destruction through logging and forest fires.