Several species of fleas (Siphonaptera), ectoparasites of mammals and birds, have recently been shown to harbor species of Wolbachia. Here, we extend this data set to 20 more species of Siphonaptera (Rhopalopsyllidae, Stephanocircidae, Pulicidae, Ceratophyllidae, Ctenophthalmidae, Ischnopsyllidae, Leptopsyllidae, and Malacopsyllidae) from sylvatic populations throughout the Nearctic and Neotropical regions. Using polymerase chain reaction, we targeted the Wolbachia 16S ribosomal DNA (rDNA) gene. Applying maximum parsimony– and maximum likelihood–based algorithms, as well as statistical parsimony, we conducted a phylogenetic analysis of Wolbachia 16S rDNA to evaluate its position within the known Wolbachia spp. The analysis recovered the siphonapteran Wolbachia 16S rDNA sequences as a monophyletic group and shows multiple haplotype connections between the Neotropical and Nearctic Wolbachia strains of fleas.