Background: Darfur in Western Sudan has the most volatile camps of internally displaced persons (IDPs) and has experienced several outbreaks of dengue, chikungunya and yellow fever. Aims: To determine the prevalence and Stegomyia indices of Aedes aquatic stages in El Geneina town, Western Darfur. Methods: Cross-sectional entomological surveys of immature stages of Aedes were carried out during August–November 2019 in 4 sites with IDP camps and a residential area with no camp. Results: We searched 17 730 houses, IDP camps and buildings of governmental corporations for Aedes larvae, and 6809 (38.4%) were positive for Aedes aquatic stages. Both Aedes aegypti and Aedes vittatus larvae were found. However, A. aegypti constituted > 90% of the larvae. Six positive water containers were recorded: tyres, clay pots, barrels, plastic water tanks, flower vases and old cars: 26% of 92 tyres contained Aedes larvae compared to 23.8% of 21 old cars and 17.1% of 44 198 clay pots. This suggested that clay pots were the main source of Aedes. The results showed high infestation of El Geneina town with Aedes immature stages in all study sites including public buildings and residential areas with no IDP camps. Stegomyia indices varied among study sites, and were more elevated in sites with IDP camps. For all sites, House index = 38.40, Container Index = 11.40, Breateu index = 13.60 and Pupa Index = 27. Conclusion: Multisectoral response coupled with community participation are urgently needed to reduce the burden of Aedes-borne diseases in the unstable El Geneina town.