Wolbachia pipientis is an intracellular endosymbiont producing reproductive alterations in its hosts. This bacterium have been reported in many arthropods and nematodes. By PCR amplification and sequencing of the 16S rDNA and ftsZ genes we have identified a Wolbachia strain in the newly described sand-flea, Tunga trimamillata. Prevalence of this endosymbiont in the 26 individuals screened is equal to 35%. Sympatric and allopatric specimens of the related species Tunga penetrans were also analysed, but in contrast to literature data, Wolbachia appears absent in the presently analysed 24 specimens. Field studies evidence a female-biased sex-ratio in T. trimamillata, suggesting that Wolbachia may cause sex-ratio distortion in this species. By means of BLAST search and phylogenetic analysis we found that the Wolbachia strain from T. trimamillata pertains to the arthropod-infecting Wolbachia; this strain is highly differentiated from the Wolbachia strain of T. penetrans described in literature.