Mosquitoes of the Anopheles gambiae species complex are the main African vectors of the human malaria parasite, Plasmodium falciparum, which is responsible for significant human morbidity and mortality. Several studies have shown the composition of the prokaryotic microbiota of Anopheles mosquitoes. However, the eukaryotic microbiota is poorly described. Here, we undertake to identified this eucaryotic miocrobiome of different species of anopheleine mosquitoes and look at their impact on mosquitoes’ infection by malaria parasite under natural condition. We hypothesized that, this microbiome varies under different environmental condition and enhance mosquitoes immune system. The outcome of this research is to collect extensive data on eukaryotic microbiome and identified the ones link to infection rate in mosquitoes