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Background  Understanding the ecology of larval malaria and lymphatic filariasis mosquitoes in a changing environment is important in developing effective control tools or programmes. This study characterized the breeding habitats of  Anopheles  mosquitoes in rural communities in different ecological zones in Ghana during the dry and rainy seasons.    Methods  The spatio-temporal distribution, species composition, and abundance of larval  Anopheles  mosquitoes in breeding habitats were studied in five locations in three ecological zones of Ghana. These were Anyakpor (coastal savannah area), Duase (forest area), and Libga, Pagaza, and Kpalsogu (Sahel savannah area). Larvae were collected using standard dippers and were raised in the insectary for identification.    Results  Out of a total of 7984 mosquito larvae collected, 2152 (27.26%) were anophelines and were more abundant in the rainy season (70.82%) than in the dry season (29.18%). The anophelines comprised 2128 (98.88%)  An. gambiae  s.l., 16 (0.74%)  An. rufipes , and 8 (0.37%)  An. pharoensis . In the coastal savannah and forest zones, dug-out wells were the most productive habitat during the dry (1.59 larvae/dip and 1.47 larvae/dip) and rainy seasons (11.28 larvae/dip and 2.05 larvae/dip). Swamps and furrows were the most productive habitats in the Sahel savannah zone during the dry (0.25 larvae/dip) and rainy (2.14 larvae/dip) seasons, respectively.  Anopheles coluzzii  was the most abundant sibling species in all the ecological zones.  Anopheles melas  and  An. arabiensis  were encountered only in the coastal savannah and the Sahel savannah areas, respectively. Larval habitat types influenced the presence of larvae as well as larval density ( p  < 0.001). The land-use type affected the presence of  Anopheles  larvae ( p  = 0.001), while vegetation cover influenced larval density ( p  < 0.05).    Conclusion  The most productive habitats were dug-out wells in the coastal savannah and forest zones, and furrows from irrigated canals in the Sahel savannah zone.  Anopheles coluzzii  was the predominant vector species in all the ecological zones. The abundance of  Anopheles  breeding habitats and larvae were influenced by anthropogenic activities. Encouraging people whose activities create the larval habitats to become involved in larval source management such as habitat manipulation to stop mosquito breeding will be important for malaria and lymphatic filariasis control.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04701-w.

Larval habitat diversity and Anopheles mosquito species distribution in different ecological zones in Ghana