Gut microbial communities of mosquitoes can influence vector susceptibility to pathogens, yet the factors that govern their composition remain poorly understood. We investigated the impact of host blood-meal source on gut microbiota of Aedes aegypti L. Adult mosquitoes were fed on human, rabbit or chicken blood and their gut microbiota compared to those of sugar-fed and newly emerged adults. Microbial diversity was significantly reduced in blood-fed and sugar-fed mosquitoes but was restored to the levels of newly emerged adults at 7-days post-blood meal. Microbial composition was strongly influenced by host blood-meal source. Leucobacter spp., Chryseobacterium spp., Elizabethkingia spp. and Serratia spp. were characteristic of newly emerged adults and adults fed on chicken, rabbit and human blood, respectively. Sugar-fed mosquitoes had higher abundance of Pseudomonas spp. and unclassified Acetobacteraceae. Shifts in gut microbial communities in response to host blood-meal source may fundamentally impact pathogen transmission given the well-documented link between specific bacterial taxa and vector susceptibility to a variety of mosquito-borne pathogens and may be a key determinant of individual and population variation in vector competence.