Despite recent efforts, hypothesised phylogenetic relationships among apocritan wasps remain unresolved. In this study, molecular analyses were employed to analyse a dataset that included the 16S, the 28S and the COI genes of 87 apocritan representatives. Partial sequences of the 18S gene were also generated and added to this dataset. The topological effects of outgroup choice, method of phylogenetic analysis, and inclusion of the 18S data were systematically investigated, with particular focus on the relationship of the Chalcidoidea with other members of the Proctotrupomorpha (Platygastroidea, Proctotrupoidea, Cynipoidea). We report that ingroup topology was sensitive to the choice of outgroup, the method of phylogenetic analysis, and inclusion of 18S data. However, the Proctotrupomorpha were always monophyletic, and the Chalcidoidea were recovered, in every analysis except one, as the sister to the diaprioid complex (Diapriidae + Monomachidae + Maamingidae). The single exception, where the Chalcidoidea + Platygastroidea were recovered, utilised a more distant outgroup (Symphyta : Cephidae : Hartigia), maximum parsimony, and excluded the 18S data. Our results suggest the Chalcidoidea + (Diapriidae + Monomachidae + Maamingidae) relationship is more likely.