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Wolbachia are obligatory, cytoplasmatically inherited α-Proteobacteria which are known for infecting the reproductive tissues of many arthropods. Their prevalence in the large group of Collembola, however, is not known, except for PCR detection in the parthenogenetically reproducing species Folsomia candida (Order: Entomobryomorpha; Family: Isotomidae). In this study, fluorescence in situ hybridization on microscopic sections of F. candida specimens indicated that Wolbachia-related bacteria were restricted to tissues of the ovary and brain. PCR with primers designed to detect 16S rRNA genes of Wolbachia were positive with specimens from all of five geographically independent F. candida breeding stocks and with three parthenogenetic species from another order (Poduromorpha; Family Tullbergiidae), i.e. Mesaphorura italica, M. macrochaeta and Paratullbergia callipygos. In contrast, negative results were obtained with the two sexually reproducing species, Isotoma viridis (Isotomidae) and Protaphorura fimata (Poduromorpha; Onychiuridae). The ftsZ gene of Wolbachia could be PCR-amplified from all Wolbachia-positive hosts with the exception of M. macrochaeta. The phylogenetic distances of the ftsZ and 16S rRNA gene sequences reflected the phylogenetic distances of the host organisms but the sequences of Wolbachia were relatively closely related, indicating that Wolbachia infections took place after the Collembola had diversified. Our study confirms a monophyletic branch (supergroup E) of Collembola colonizing Wolbachia and indicates that this group is a sister group of supergroup A, the latter harbouring a high diversity of host organisms within the group of insects.