Recent studies have highlighted associations between diseases and host microbiota. It is yet extremely challenging-especially under natural conditions-to clarify whether the host microbiota promotes future infections, or whether changes in host microbiota result from infections. Nonetheless, deciphering between these two processes is essential for highlighting the role of microbes in disease progression. We longitudinally surveyed, in the wild, the microbiota of individual fish hosts (Leuciscus burdigalensis) both before and after infection by a crustacean ectoparasite (Tracheliastes polycolpus). We found a striking association between parasite infection and the host microbiota composition restricted to the fins the parasite anchored. We clearly demonstrated that infections by the parasite induced a shift in (and did not result from) the host fin microbiota. Fin microbiota further got similar to that of the adult stage, and the free-living infective stage of the parasite during infection with a predominance of the Burkholderiaceae bacteria family. This suggests that Burkholderiaceae bacteria is involved in a co-infection process and possibly facilitate T. polycolpus infection. We reveal novel mechanistic insights for understanding the role of the microbiota in host-parasite interactions, which has implications for predicting the progression of diseases in natural host populations.