This study was performed to investigate Wolbachia endobacteria in Culex pipiens specimens collected from Kayseri province of Turkey. For this aim, totally 10 genomic DNA pools each including 6-15 Cx. pipiens specimens which were collected and identified within the scope of a project (No: 1070533) supported by TUBITAK, were examined by using the amplification of surface protein gene (wsp) region of the Wolbachia. The sequences from this gene were highly variable and could be used to resolve the phylogenetic relationships of different Wolbachia strains. After the genomic DNA extraction from the pools, PCR analyses were carried out with Wolbachia specific primer pair which was amplified a 590-632 bp region of the wsp gene. Out of 6 of the 10 examined genomic DNA pools were found to be positive (60.0%) by PCR analyses. The minimum infection rate of Wolbachia spp. in the totally analyzed 118 Cx. pipens specimens was determined as 5.08. One of the amplicon from the positive isolates was gel purified and sequenced in terms of wsp gene region of Wolbachia by using the same primers. Pair wise analyses of the obtained DNA sequences and multiple alignments with some other Wolbachia strains available in the GenBank were done and phylogenies were investigated. The obtained isolate (WolKys1) was deposited in GenBank International Nucleotide Sequence Database with the accession number JX474753. The phylogenetic analyses revealed that the obtained WolKys1 isolate belongs to Wolbachia Super Group B and wPIP group. According to the phylogenetic comparisons the WolKys1 showed 100.0% identity with some other Wolbachia isolates under the Group B. In conclusion, this study reports the first molecular detection and characterization of Wolbachia endobacteria in Cx. pipiens populations in Turkey.