Microbiota in the mosquito plays an important role in their behavior and vector competence. The composition of their microbiome is strongly influenced by the environment, especially their habitat. The microbiome profiles of adult femaleAnopheles sinensismosquitoes from malaria hyperendemic and hypoendemic areas in Republic of Korea were compared using 16S rRNA Illumina sequencing. In different epidemiology groups, the alpha and beta diversity analyses were significant. The major bacterial phylum was Proteobacteria. The most abundant species in the microbiome of hyperendemic mosquitoes were the generaStaphylococcus,Erwinia,Serratia, andPantoea. Notably, a distinct microbiome profile characterized by the dominance ofPseudomonas synxanthawas identified in the hypoendemic area, suggesting a potential correlation between the microbiome profiles and the incidence of malaria cases.