The present study was designed to investigate the seasonal abundance of Culex pipiens and Culex antennatus aquatic larvae in Fayoum Governorate, Egypt. The study was carried out in the En Nazla region, Ibshway during the winter, spring, summer and autumn of 2021. In addition, the physicochemical parameters of breeding water habitats were evaluated during different seasons, and relationships between measured parameters and mosquito abundance were addressed. PCR and sequencing confirmed the genetic identification of both Culex species. Generally, C. pipiens was more abundant than C. antennatus in the study area. Summer recorded the highest abundance for both C. pipiens and C. antennatus (about 683 and 400 larvae), superior to what has been recorded in other seasons with a significant margin (P< 0.05), while winter recorded the lowest abundance of both mosquito species. The highest correlation between seasons for C. pipiens calculated an abundance between winter and autumn (0.83), while the lowest was recorded between winter and summer (0.22). Data assessed revealed that the TDS is the most reliable factor that mosquito abundance depends on, followed by the pH value for C. pipiens and temperature for C. antennatus. On the other hand, C. pipiens showed a clear relationship with species identified from Portugal and Kenya, with an evolutionary distance of approx. 0.001164. Moreover, Cx antennatus displayed a close relationship to a species identified from Madagascar and Kenya, with an evolutionary distance of approx. 0.00734, respectively.