Phylogenetic relationships among 95 genera collectively representing 17 of the 18 currently recognized cyclostome braconid wasp subfamilies were investigated based on DNA sequence fragments of the mitochondrial COI and the nuclear 28S rDNA genes, in addition to morphological data. The treatment of sequence length variation of the 28S partition was explored by either excluding ambiguously aligned regions and indel information (28SN) or recoding them (28SA) using the 'fragment-level' alignment method with a modified coding approach. Bayesian MCMC analyses were performed for the separate and combined data sets and a maximum parsimony analysis was also carried out for the simultaneous molecular and morphological data sets. There was a significant incongruence between the two genes and between 28S and morphology, but not for morphology and COI. Different analyses with the 28SA data matrix resulted in topologies that were generally similar to the ones from the 28SN matrix; however, the former topologies recovered a higher number of significantly supported clades and had a higher mean Bayesian posterior probability, thus supporting the inclusion of information from ambiguously aligned regions and indel events in phylogenetic analyses where possible. Based on the significantly supported clades obtained from the simultaneous molecular and morphological analyses, we propose that a total of 17 subfamilies should be recognized within the cyclostome group. The subfamilial placements of several problematic cyclostome genera were also established.