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Many studies have highlighted how numerous bacteria provide their hosts essential nutrients or protection against pathogens, parasites and predators. Nevertheless, the role of symbiotic microorganisms in the interactions between social insects and their parasites is still poorly known. Microdon (Diptera, Syrphidae) is a peculiar fly genus whose larvae are able to successfully infiltrate ant colonies and feed upon the ant brood. Using high throughput 16S rRNA gene amplicon sequencing, we provide the first microbiome survey of Mi. myrmicae larvae and larvae and workers of its host, Myrmica scabrinodis, collected from two sites in England. We analyzed the microbiome of the external surface of the cuticle and the internal microbiome of the body separately. The results clearly show that the Mi. myrmicae microbiome significantly differs from that of its host, while no substantial dissimilarity was detected across the microbiome of ant workers and ant larvae. Microdon myrmicae microbiome varies across the two analyzed sites suggesting that bacteria communities of Mi. myrmicae are derived from the environment rather than by horizontal transmission between hosts and parasites. Families Streptococcaceae, Carnobacteriaceae and Rizhobiaceae are dominant in My. scabrinodis, and Spiroplasma is dominant in ant workers. Microbiome of Mi. myrmicae larvae is mainly characterized by the family Anaplasmataceae, with Wolbachia as predominant genus. Interestingly, we found Serratia within both Mi. myrmicae and Myrmica larvae. Bacteria of this genus are known to produce a family of pyrazines commonly involved in ant communication, which could play a role in Microdon/ant interaction.