Following their transmission from the human to the mosquito with the bloodmeal, malaria parasites have to persevere in the mosquito midgut for approximately 1 d. During this period the parasites are highly vulnerable to factors of the mosquito midgut, including bacteria. We here aimed at determining the microbial diversity of gut bacteria of the Asian malaria vector Anopheles stephensi (Liston) during development and under different feeding regimes, including feeds on malaria parasite-infected blood. 16S rRNA and denaturing gradient gel electrophoresis analyses demonstrated an increasing reduction in the microbial diversity during mosquito development from egg to adult and identified the gram-negative bacterium Elizabethkingia meningoseptica King as the dominant species in the midgut of lab-reared male and female mosquitoes. E. meningoseptica is transmitted between generations and its predominance in the mosquito midgut was not altered by diet, when the gut microbiota was compared between sugar-fed and blood-fed female mosquitoes. Furthermore, feeds on blood infected with malaria parasites did not impact the presence of E. meningoseptica in the gut. Extracts from cultured E. meningoseptica were active against gram-positive and negative bacteria and yeast and against the blood and gametocyte transmission stages of the malaria parasite Plasmodium falciparum Welch. The antimicrobial and antiplasmodial activities of E. meningoseptica may account for its dominance in the midgut of the malaria vector.