Aedes aegypti is the main vector for dengue, chikungunya, yellow fever, Zika, and other arboviruses of public health importance. The presence of Ae. aegypti has never been systematically assessed in Zanzibar, including its preferred larval habitats. In 2016 we conducted a cross-sectional entomological survey to describe the preferred larval habitats of Ae. aegypti in Zanzibar City, the main urban area of the Zanzibar archipelago. The surveys for container habitats were conducted for a 17-wk period beginning in January 2016. Immature stages (larvae and pupae) were collected, reared to adulthood, and identified to species. The positive and potential habitats were categorized on the basis of physical, biological, and chemical parameters. A total of 200 samples were collected, of which 124 (62.0%) were positive for immature stages of mosquitoes and 114 (92%) for Ae. aegypti larvae and pupae. Presence of vegetation (odds ratio [OR] ¼ 2.11, 95% confidence interval [CI] ¼ 1.19– 3.74), organic matter (OR ¼2.37, 95% CI ¼1.21–4.60), inorganic matter (OR ¼1.78, 95% CI ¼1.01–3.13), and sun exposure (OR¼2.34, 95% CI¼1.24–4.36) were all significantly associated with the presence of immature stages of Ae. aegypti, suggesting that these conditions promote colonization of containers. Plastic containers supported 64% of the immature stages and produced approximately 50% of the pupae. Although immature counts were the highest in discarded artifacts, higher pupal counts were found in domestic water storage containers. Our observations suggest that effective control of Ae. aegypti in Zanzibar City must include improved solid waste management (collection and proper disposal of potential container habitats) and reliable supply of domestic water to minimize water-storing practices that provide larval habitats for Ae. aegypti.