Wolbachiapipientis is an obligate intracellular endosymbiont that commonly infects arthropods. Comparative genomic studies of Wolbachia reveal traces of numerous events of intergenic and intragenic recombination. The molecular mechanisms of recombination in Wolbachia are not currently known. We conducted experimental verification of the possibility of recombination of two strains of Wolbachia: wMel and wRi, after using these strains for double infection of the Dm2008Wb1 (D. melanogaster) cell culture clone permissive to Wolbachia. We obtained cell culture subclones with double Wolbachia infection and subclones infected only by strain wMel. Dual infection with the Wolbachia strains wMel and wRi has been stably maintained in the subclones for two years. Multilocus sequence typing (MLST) of the obtained subclones revealed the presence of dual infection for all five Wolbachia genes used for MLST Cloning and nucleotide sequence analysis of individual forms of the fbpA gene of Wolbachia from cell clones with dual infection showed intragenic recombination events between strains wMel and wRi, which occurred in the permanent D. melanogaster culture cell culture. The fact that putative recombination sites contain no insertions of nucleotide sequences of phages or IS elements, as well as the asymmetrical character of recombinants, favors the hypothesis that gene conversion is the most probable molecular mechanism of recombination in Wolbachia.