The Doryctinae is one of the most specious subfamilies of the mainly parasitoid wasp family Braconidae. Members of this subfamily are characterised by having a very heterogeneous external morphology, which has made establishing the limits of several of its genera extremely difficult. The Neotropical Callihormius Ashmead, Platydoryctes Barbalho & Penteado-Dias, and Aphelopsia Marsh are prime examples of this, since they show extensive interspecific morphological variation but lack consistent diagnostic features among them. We carried out a comprehensive phylogenetic study among several representative species belonging to the above genera as well as other morphologically similar doryctine taxa based on three nuclear and two mitochondrial (mt)DNA sequence markers. Based on the relationships recovered, we assessed the generic limits among the examined taxa and investigated the times of origin and diversification in this group. Our best estimate of phylogeny did not recover Callihormius as monophyletic, and thus we propose a taxonomic arrangement where we elevate the status of Ca. (Dmitriohormius) Belokobylskij, Zaldívar-Riverón & Coronado-Blanco to genus level, stat. nov., and also describe four new genera: Macrometasoma, gen. nov., Caputlenis, gen. nov., Platyhormius, gen. nov. and Caputrugosus, gen. nov.Platydoryctes is delimited morphologically, and the body flatness is proposed to have independently evolved more than once within the group of genera examined. Aphelopsia was not recovered as monophyletic, though the relationships involved were weakly supported and therefore we maintain its species composition. Panama Marsh, stat. rev., which was considered a junior synonym of Leluthia Cameron, is resurrected. Basal relationships in the phylogeny had very short branch lengths, which could be due to ancient rapid radiation events that occurred during the early evolution of the group. The estimated times of divergence showed that the clade containing Callihormius and its related genera originated between the late Oligocene and middle Miocene, whereas its early diversification events probably occurred between the middle to late Miocene.