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Abstract Background Interaction of microinvertebrates with mosquito in freshwater ecosystem ultimately provides the mosquito larvae with diverse resources to prey on and serves as competitors or predators. The trophic ecology and productivity of mosquito larvae in rock pool habitats are paramount to modelling and predicting adult mosquito abundance and ultimately limit their disease spread. Results Fine mesh plankton net and soup ladle dipper were used to obtain microinvertebrates and preimaginal mosquitoes respectively in 368 rock pools on inselbergs in 21 settlements within Kaduna State, Nigeria. A total of 31,726 mosquito larvae bred in 269 rock pools coinhabited with microinvertebrates. Diluted ethanol (70%) and formaldehyde (4%) were used to preserve mosquito and microinvertebrate specimens, respectively. Specimens of mosquito larvae and microinvertebrates were identified using standard keys. Pearson’s correlation analysis was used to establish the relationship between abundances of mosquitoes and microinvertebrates. Thirty species of microinvertebrates coinhabited with six species of mosquito (Aedes vittatus, Anopheles gambiae s.l., Culex macfiei, Cx. perfidiosus, Cx. pipiens pipiens, and Cx. simpsoni). The microinvertabrates included the protozoans: Paramecium caudatum (Parameciidae) and Pleurotricha sp. (Oxytrichidae); Chlamydomonas reinhardtii; the rotifers: Brachionus plicatilis (Brachionidae) and Philodina sp. (Philodinidae); the sponge (Porifera): Heteromeyenia tenosperma (Spongillidae); the crustaceans: Ephemeroporous barroisi (Chydoridae), Bosmina longirostris (Bosminidae), Daphnia pulex (Daphniidae), Diaphanosoma birgei (Sididae), Diaphanosoma brachyurum, Laptonopsis occidentalis, Macrothrix pulex (Macrothricidae), Macrothrix rosea, Moinodaphnia macleayi (Moinidae), Moina macrocopa (Moinidae), Sida crystallina (Sididae), Bradleystrandesia reticulata (Cyprididae), Candona intermedia (Candonidae), Candona parallela, Cypria obesa (Cyprididae), Heterocyp.ris incongruens (Cyprididae), Potamocypris hyboforma (Cyprididae), Cyclops sp. (Cyclopidae), and Macrocyclops sp. (Cyclopidae); and the nematodes: Alaimus sp. (Alaimidae), Diplogaster sp. (Diplogasteridae), Monhystera sp. (Monhysteridae), and Rhabdolaimus sp. (Rhabdolaimidae). Mosquitoes relative abundance correlated negatively but significantly (P |