Out of 400 mosquito specimens collected from Sultan Marshes ecosystem m Kaysen, 296 (74.0%) were identified as Culex pipiens, 63 (15.75%) as Aedes vexans, and 41 (10.25%) as Culiseta annulata. Individual DNA was extracted from adult mosquitos and PCR analysis was performed m terms of the wsp gene region. While Wolbachia positivity was detected in 119 (40.2%) female Cx. pipiens, none of the male Cx. pipiens specimens were positive. No positivity was detected in Ae. vexans and Cs. annulata samples. In the phylogenetic analyzes of the 10 isolates selected from Wolbachia positive samples, the EruWolCpip1-10 isolates were clustered m the Wolbachia B supergroup and wPip group. It was found that EruWolCpip1-9 isolates were 100% identical among themselves and these isolates genetically differed by 0.5% with EruWolCpip10 isolate. The previous isolates of WolKys1 isolated from Cx. pipiens in Kaysen region and TrERUWolLice isolated from Bovicola limbata in Cankiri region have 100% similarity with EruWolCpip1-9 isolates. It was also determined that the EruWolCpip1-9 isolates were 100% identical with the Cx. pipiens, Penbadotes rhomboidaria, Agriocnemis femina femina and Eurema hecabe Wolbachia isolates m the wPip group. Furthermore, while the genetic difference within the wPip group was 0.28 +/- 0.11%, the genetic difference between the Dei, Con and Ori gioups which placed in the same super group with the wPip gioup was found as 16.9 +/- 2.3, 12.5%+/- 1.9% and 19.9 +/- 25%, respectively. The genetic difference between Haw, Riw. Mel, Aus, Mors, Uni, Pap and Alba groups in the A super group, and the wPip group in the B super group were determined as 23.5 +/- 3.0%, 17.6 +/- 2.3%, 19.1 +/- 2.5%, 22.0 +/- 2.8%, 21.0 +/- 2.7%, 22.3 +/- 2.9%, 22.0 +/- 2.8% and 20.5 +/- 2.6%, respectively. This study was carried out with the hypothesis that the genetic difference between Wolbachia isolates obtained from different arthropod species in different geographical regions and classified in the same or different super groups, and our isolates may be significant. As a result, while the genetic difference between the isolates m the same groups was found less significant, the genetic difference in different super groups was determined much more significant. These results confirmed our hypothesis.