Wolbachia pipientis (w Pip) is an intracellular bacterium causing cytoplasmic incompatibility in arthropods including mosquitoes of the Culex pipiens complex. Here we present a method useful for genotyping within the w Pip group. Primers were designed using a Tandem Repeat Finder program to amplify an intergenic, polymorphic site (pp-hC1A_5) of w Pip. The polymorphic site is located between genes that code for polynucleotide phosphorylase and a hypothetical protein (C1A_5). Comparison of these w Pip genomic regions from C. pipiens mosquitoes sampled in different geographic regions revealed deletions of fragments that proved useful in phyologenetic analysis.