Host discrimination by immature host-seeking endoparasites is a complex and somewhat unexplored topic. In the case of multiple infections, conflicts among conspecifics may occur to monopolize space and resources in the same host. Two or more 1st instar larvae of Xenos vesparum (Strepsiptera, Stylopidae) may enter into a Polistes dominulus (Hymenoptera, Vespidae) larva and develop together until the adult stage of both parasite and host. We carried out a screening of mitochondrial haplotypes in X. vesparum individuals extracted from superparasitized wasps taken in 5 naturally infected nests from different areas of Tuscany (Italy), to assess whether non-sibling parasites may infect the same colony and host. In total, we obtained 12 different haplotypes out of 122 genotyped individuals of both sexes: 17 of 34 superparasitized wasps hosted parasites that originated from females differing in their haplotypes. To date, this is the first described case of superparasitism with non-sibling host-seeking larvae infecting a single individual hymenopteran host. In addition, at least in heavily infected colonies, there is evidence of a male-biased sex-ratio and synchronous development of the parasites, regardless of their haplotypes. Finally, the distribution of haplotypes per nest is consistent with either phoretic infection or larvipositing on nests by means of superparasitized wasps.