The microbial flora associated with fleas may affect their ability to transmit specific pathogens, including Yersinia pestis, and also could be used to develop paratransgenesis-based approaches to interfere with transmission. To begin addressing this hypothesis, the microbial flora associated with the relatively efficient Y. pestis vectors Xenopsylla cheopis (Rothschild) (Siphonaptera: Pulicidae) and Oropsylla montana (Baker) (Siphonaptera: Ceratophyllidae), and the inefficient vector Ctenocephalides felis felis (Bouché) (Siphonaptera: Pulicidae) were investigated using polymerase chain reaction amplification of 16S rDNA genes. DNA sequencing revealed that these species harbor distinct communities of microbial flora and suggest that Acinetobacter sp. might be used in developing anti-transmission strategies.