Detecting interaction between species is notoriously difficult, and disentangling species associations in host-related gut communities is especially challenging. Nevertheless, due to contemporary methods, including metabarcoding and 16S sequencing, collecting observational data on community composition has become easier and much more common. We studied the previously collected data sets of intestinal microbiota and parasite compositions within longitudinally followed mouse lemurs by analysing the potential interactions with diversity metrics and novel joint species distribution modelling. Both methods showed consistent statistical association between certain parasite species and microbiotal composition. Both unicellular Eimeria sp. and cestode Hymenolepis diminuta had an effect on diversity of gut microbiota. These parasite species also had negative associations with several bacterial orders. In comparison, closely related species H. nana did not have an effect on diversity, and it had positive associations with several bacterial orders. Our results reveal potential interactions between some, but not all, intestinal parasites and gut microbiota. While environmental variables explained almost half of the total variation, of which almost half could be explained by traits of parasites and microbiota, there were no clear patterns regarding mouse lemur individual variables explaining variation in the occurrence patterns of parasite and microbiota significantly. Our results provide new hypothesis for interactions between and among parasites and microbiota to be tested further with experimental studies.