BACKGROUND: Microsporidians (Microsporidia) are a group of obligate intracellular parasites that commonly infect mosquitoes. Recently, it has been shown that infection by these parasites can alter the composition and functionality of the mosquito-associated microbiome. The host-associated microbiome of the mosquito can play a pivotal role in various physiological processes of this host, including its vector competence for pathogens. Thus, understanding how microsporidians shape the mosquito microbiome may be crucial for elucidating interactions between these parasites and their mosquito hosts, which are also vectors for other parasites and pathogens. METHODS: The effects of microsporidian infection on the microbiome structure and functionality of Culex pipiens and Culex torrentium larvae under semi-natural conditions were examined. The host-associated microbiome of Cx. pipiens (n = 498) and Cx. torrentium (n = 465) larvae, including that of the 97 infected individuals of these samples, was analysed using 16S DNA profiling and functional prediction analysis. RESULTS: Microbiome network analysis revealed that, in the microsporidian-positive larvae, host microbial communities consistently grouped within a common bacterial module that included Aerococcaceae, Lactobacillaceae, Microbacteriaceae, Myxococcaceae, and Polyangiaceae. Indicator species analysis revealed two strong positive correlations between microsporidian infection and the presence of Weissella cf. viridescens and Wolbachia pipientis. Functional predictions of microbiome content showed enrichment in biosynthetic pathways for ansamycin and vancomycin antibiotic groups in infected larvae. Furthermore, the MexJK-OprM multidrug-resistance module was exclusively present in the infected larvae, while carbapenem- and vancomycin-resistance modules were specific to the microsporidian-free larvae. CONCLUSIONS: Our results demonstrate that microsporidian infection alters the microbial community composition in mosquito larvae. Moreover, they show that microsporidian infection can increase the antimicrobial capabilities of the host-associated microbiome. These results provide novel insights into host microbiome-parasite interactions and have potential implications for the vector competencies of mosquitoes.