We present the first species-level molecular phylogenetic hypothesis for the Asian trogons, using DNA sequences of multiple mitochondrial and nuclear loci, and Bayesian and maximum likelihood tree reconstruction methods. The two genera of Asian trogons, Harpactes and Apalharpactes, are distantly related to each other. Within the widespread Southeast Asian genus Harpactes, we recovered three species groups: (1) H. oreskios; (2) H. orrhophaeus and H. duvaucelii; and (3) a clade of the seven large-bodied species. Short internal branch lengths link species in the large-bodied group, suggesting rapid diversification. Apalharpactes, which is currently restricted to the montane forests of Sumatra and Java, appears to be a relictual lineage distantly related to all other trogons. Bayesian and maximum likelihood analyses indicate Apalharpactes is sister to the African genus Apaloderma, although this result was not strongly supported. Overall, the extant Asian trogon species appear to have diversified prior to the Pleistocene, based on large pair-wise mitochondrial divergences between taxa.