Members of the tribe Baeini are unique among the Scelonidae as endoparasitoids of the eggs of spiders, whereas all other scelionids parasitise insect eggs. The monophyly of the Baeini has previously been assumed based on this host association and several morphological characteristics, none of which are unequivocal. Here we present a phylogeny for the group using sequence data from two genes and 32 ingroup taxa, mostly from Australia. Combined analysis of the nuclear 28S rRNA gene and the mitochondrial CO1 gene showed that the tribe is not monophyletic, because two genera (Neobaeus Austin and Mirobaeoides Dodd) are resolved in a clade separate from the rest of the Baeini. The two most speciose genera, Idris Foerster and Ceratobaeus Ashmead, are not resolved as monophyletic, indicating that a metasomal horn, which acts as a recess for the internally retracted ovipositor, has evolved multiple times within the tribe. Mapping of wing reduction states that occur in the Baeini revealed multiple wing reduction events, possibly associated with adaptations for searching for host egg masses in crytobiotic habitats, and/or penetrating the silk egg sacs of spiders. The molecular phylogeny generated in this study differs significantly from previous morphological phylogenies, and has resolved relationships that have otherwise been intractable in morphological studies because of homoplasy associated with reduction in body size.