BackgroundLarval source management (LSM), which requires an understanding of the ecology and composition of the local mosquito fauna, is an important parameter in successful vector control programmes. The present study was conducted to understand the distribution of larval habitats, species composition and factors associated with the seasonal abundance of mosquito larvae in Gezira irrigation Scheme in Gezira state, central Sudan.MethodsCross-sectional larval surveys were carried out in the communities of Barakat (urban) and El-Kareiba (semi-urban), in Wad Madani, Gezira. A standard dipper was used for sampling larvae in all possible breeding sites and enamel bowls were employed for larvae sorting. Habitats were characterised using physical features and all larvae specimens were identified morphologically.ResultsA total of 331 larval habitats were surveyed, out of which 166 were found to be positive breeding sites for Anopheles (56.78%), Culicinae (29.67%) and Aedes (13.55%) species. A total of 5 525 larvae collected were categorised as Culex (2 617, 47.37%), Anopheles (2 600, 47.06%) and Aedes (308, 5.57%). There was a high number of positive habitats during the rainy season, while the lowest proportion was reported during the hot dry season, in both study sites (Barakat [χ
2 = 10.641, P = 0.0090], El-Kareiba [χ
2 = 23.765, P = 0.0001]). The main breeding site for Anopheles larvae was leaking water pipes (51.5%), followed by irrigation channels (34.2%), hoof prints (6.4%), tyre tracks (5.5%) and water tanks (2.4%). A logistic regression analysis showed that the abundance of Anopheles larvae was reduced by the presence of predators (backswimmers, tadpoles) and grass cover. Adult productivity (number of adult females emerged/m2) was not homogeneousfor all habitats; the highest productivity was found in irrigation channels (0.78 females/m2) for Anopheles, and in septic tanks (2.86 females/m2) for Culicinae and (0.86 females/m2) for Aedes. Anopheles arabiensis was found to be the dominant Anopheles species. This study documented the presence of An. funestus in central Sudan for the first time.ConclusionsMaintaining leaking water pipes and adopting intermittent irrigation are recommended for LSM, as these surveyed habitats represent the main source of maintaining the local mosquito population during the hot dry season.Electronic supplementary materialThe online version of this article (doi:10.1186/s40249-017-0242-1) contains supplementary material, which is available to authorized users.