The short–term advantages of sexual reproduction are unclear, but the existence of groups that are capable of producing either meiotic or ameiotic eggs (cyclic parthenogenesis, CP) might indicate that short–term advantages to sex exist. Alternatively, CP might be an unstable transitory stage between asexuality and sex, or a phylogenetically favoured life cycle (i.e. clade selection). The extensive knowledge of breeding systems and population genetics in branchiopod crustaceans makes them a useful group to test phylogenetic predictions of these hypotheses. Several proponents favour the hypothesis that CP has evolved multiple times in five orders of branchiopod crustaceans. We inferred the first robust branchiopod phylogeny from nuclear rRNA sequence (SSU and LSU), morphology, and complex rRNA stem–loop structures to assess the phylogenetic distribution of cyclic parthenogenesis. The sequence–based, structural rRNA and total evidence phylogenies are concordant and suggest that cyclic parthenogenesis arose once in the branchiopods, that this clade is long–lived (at least since the Permian), and that it has radiated extensively into nearly every aqueous habitat without reverting to strict sexuality and only rarely transforming to strict asexuality. These results are consistent with the clade selection hypothesis but inconsistent with the predictions of the hypothesis that CP is a transitory stage that leads to strict sexual reproduction. The evidence also indicates that clade selection for CP is a viable alternative explanation for the maintenance of sex in CP life cycles.