Introduction: The surveillance of mosquito vectors is important for the control of arboviruses diseases worldwide. Detailed information on the bionomics and distribution of their main vectors, Aedes aegypti and Aedes albopictus, is essential for assessing disease transmission risk and for better planning of control interventions. Methods: Entomological surveys were carried out from November 2019 to November 2020 in six localities of Yaoundé city following a transect from urban to rural settings: two urban (Obili, Mvan), two peri-urban (Simbock, Ahala) and two rural areas (Lendom, Elig-essomballa)—during rainy and dry seasons. All water containers were inspected. Aedes mosquito abundance, species distribution and seasonal distribution patterns were compared using generalized linear models. Stegomyia indexes were estimated to determine the risk of arbovirus transmission. Results: A total of 6332 mosquitoes larvae were collected (2342 in urban areas, 1694 in peri-urban areas and 2296 in rural sites). Aedes species recorded included Ae. albopictus, Ae. aegytpi, Ae. simpsoni and Aedes spp. High mosquito abundance was registered in the rainy season (4706) compared to the dry season (1626) (p < 0.0001). Ae. albopictus was the most abundant Aedes species in urban (96.89%) and peri-urban (95.09%) sites whereas Ae. aegypti was more prevalent in rural sites (68.56%) (p < 0.0001). Both species were found together in 71 larval habitats. Ae. albopictus was mostly found in discarded tires (42.51%), whereas Ae. aegypti was more prevalent in plastic containers used for storing water (65.87%). The majority of Aedes mosquitoes’ breeding places were situated close to human dwellings (0–10 m). Conclusion: Uncontrolled urbanization seems to greatly favour the presence of Aedes mosquito species around human dwellings in Yaoundé. Controlling Aedes mosquito distribution is becoming urgent to reduce the risk of arbovirus outbreaks in the city of Yaoundé.