Mosquitoes, the primary vectors of arboviruses, harbor a diverse microbiome that plays a crucial role in their development, immunity, and vector competence, tThe composition of the mosquito microbiome is heavily influenced by the environment and habitats, Therefore, identifying the relationship between the habitat and the mosquito's microbial community can improve the overall understanding of mosquito biology, However, the microbiome profiles of Culex tritaeniorhynchus and Culex orientalis, known as transmission vectors of the Japanese encephalitis virus, are poorly understood. Using 16s rRNA Illumina sequencing, we hereby investigated the microbial profiles in these two mosquito species collected in several areas in Korea. Thirty-six prevalent bacterial familes were identified from these mosquito species. the microbial composition variation were primarily influenced by the mosquito collecting sites. Moreover, species biomakers were identified by utilizing the regional specificity of the mosquito microbiome. Based on the microbiome profiles representing high similarity, Culex orientalis may share an ecological niche with Culex tritaeniorhynchus.