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The mosquito <i>Culex pipiens</i> occurs in two ecotypes differing in their mating and overwintering behavior: pipiens mate in open environments and diapause, and molestus also mate in small spaces and is active throughout the year. <i>Cx. pipiens</i> carry <i>Wolbachia</i> endosymbionts of the <i>w</i>Pip strain, but the frequency of infection differs between studied populations. <i>Wolbachia</i> infection affects the host reproductive success through cytoplasmic incompatibility. <i>w</i>Pip <i>Wolbachia</i> is divided into five types, <i>w</i>Pip I–V. The type of <i>w</i>Pip carried varies among <i>Cx. pipiens</i> populations. In northern European locations different <i>w</i>Pip types are found in the two ecotypes, whereas in southern locations, they often carry the same type, indicating differences in hybridization between ecotypes. In this study, <i>Cx. pipiens</i> specimens of both ecotypes were collected from Sweden and compared to specimens from Norway, England, Italy, and the Netherlands, as well as <i>Cx. quinquefasciatus</i> from Mali and Thailand. The abundance varied, but all specimens were infected by <i>Wolbachia</i>, while the tested specimens of other mosquito species were often uninfected. The <i>w</i>Pip strains were determined through the sequence analysis of <i>Wolbachia</i> genes <i>ank2</i> and <i>pk1</i>, showing that <i>Cx. pipiens</i> ecotypes in Scandinavia carry different <i>w</i>Pip strains. The observed differences in <i>w</i>Pip strains indicate that hybridization is not frequent and may contribute to barriers against hybridization of the ecotypes in Sweden and Norway.