Aedes albopictus (Diptera: Culicidae) was first reported in Central Africa in 2000, together with the indigenous mosquito species Aedes aegypti (Diptera: Culicidae). Because Ae. albopictus can also transmit arboviruses, its introduction is a public health concern. We undertook a comparative study in three Cameroonian towns (Sahelian domain: Garoua; equatorial domain: Douala and Yaoundé) in order to document infestation by the two species and their ecological preferences. High and variable levels of pre-imaginal Ae. aegypti and Ae. albopictus infestation were detected. Only Ae. aegypti was encountered in Garoua, whereas both species were found in Douala and Yaoundé, albeit with significant differences in their relative prevalence. Peridomestic water containers were the most strongly colonized and productive larval habitats for both species. No major differences in types of larval habitat were found, but Ae. albopictus preferentially bred in containers containing plant debris or surrounded by vegetation, whereas Ae. aegypti tended to breed in containers located in environments with a high density of buildings. These findings may have important implications for vector control strategies.