Despite the presence of Culex (Cx.) pipiens mosquitoes and circulation of West Nile virus (WNV), WNV outbreaks have so far not occurred in northern Europe. The species Cx. pipiens consists of two morphologically identical biotypes, pipiens and molestus, which can form hybrids. Until now, population dynamic studies of Cx. pipiens have not differentiated between biotypes and hybrids at the European scale, nor have they used comparative surveillance approaches. We therefore aimed to elucidate the relative abundance of Cx. pipiens biotypes and hybrids in three habitat types at different latitudes across Europe, using two different surveillance traps. BG-Sentinel and Mosquito-Magnet Liberty Plus traps were placed in three habitat types (farms, peri-urban, wetlands), in three European countries (Sweden, The Netherlands, Italy). Collected Cx. pipiens mosquitoes were identified to biotype with real-time PCR. Both trap types collected equal ratios of the biotypes and their hybrids. From northern to southern latitudes there was a significant decrease of pipiens and an increase of molestus. Habitat types influenced the relative ratios of biotypes and hybrids, but results were not consistent across latitudes. Our results emphasize the need to differentiate Cx. pipiens to the biotype level, especially for proper future WNV risk assessments for Europe.