Abstract. The braconid wasp genusCotesiaCameron (Braconidae: Microgastrinae) is one of the largest genera of parasitoid wasps, and its species are employed frequently as biological control agents against pest insects. SeveralCotesiaspecies are also used as model organisms in physiology, ecology and population genetics studies. The genus thus has considerable importance from both applied and basic science perspectives. We investigated the phylogenetic relationships of twenty‐five species ofCotesiacommonly used in field and laboratory research, using the genes 16S, ND1, 28S and LW opsin and employing a range of phylogeny estimation methods including maximum parsimony, maximum likelihood, minimum evolution and Bayesian inference. Phylogenetic estimates differed little among methods, especially for the combined data analysis. The combined analysis of four genes identified four well‐supported clades withinCotesia: themelanoscelagroup (containingC. melanoscela, theC. flavipesspecies complex and probably alsoC. ruficrus), thekariyaigroup (containingC. kariyai,C. kazak,C. cyaniridis,C. flaviconchaeand probably alsoC. anisotaeandC. griffini), therubeculagroup (containingC. congregata,C.electrae,C.euchaetis,C. marginiventris,C. obsuricornisandC. schizurae), and theglomeratagroup (consisting ofC. glomerata,C. melitaearumandC. plutellae), plus a basal unresolved complex includingC. hyphantriae,C. diacrisiaeandC. empretiae. These groups correspond poorly with previous broad subgroups ofCotesiadefined by Papp based on morphology. The current work constitutes the first real framework for comparative studies in systematics, ecology, physiology and population genetics ofCotesia. A preliminary analysis of the evolution of gregarious development from solitary is presented, in which it is apparent that solitary development is ancestral, and gregariousness has arisen several times independently within separate groups.