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Background   Aedes aegypti  and  Aedes albopictus  are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male  Aedes  mosquitoes. The relationship between the midgut and entire body microbiota of  Aedes  is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of  Aedes aegypti  and  Aedes albopictus  using 16S rRNA gene sequencing.    Methods  In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.    Results  A total of 341 OTUs were identified, showing that  Proteobacteria  was the dominant phylum and  Methylobacterium  the dominant genus in both  Aedes aegypti  and  Aedes albopictus . The bacterial diversity and community structures of the entire bodies were similar between males and females in both  Aedes aegypti  and  Aedes albopictus . Conversely, the bacterial compositions of male and female  Aedes aegypti  and  Aedes albopictus  were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of  Aedes aegypti  and  Aedes albopictus . Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female  Aedes albopictus  and  Aedes Aegypti .    Conclusions  Our findings that  Aedes aegypti  and  Aedes albopictus  reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of  Aedes  mosquitoes.    Graphical abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-05050-4.

Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China