The symbiotic relationship between macroorganisms, such as plants and animals, and the microorganisms in their environment plays a crucial role in shaping their physiology and ecology. Thus, many studies have examined microbial symbiosis in relation to plants, humans, and insects. However, little is known about the microbial diversity associated with isopods. Hence, in this study, we investigated the fungal diversity associated with two species of terrestrial isopods, Armadillidium nasatum and A. vulgare. In this study, we used a metabarcoding approach to compare fungal diversity between the two species for the first time. Our results indicated that A. nasatum had significantly greater mycobiome alpha diversity than A. vulgare. In contrast, fungal communities (beta diversity) did not differ significantly between hosts, except in beta dispersion of relative abundance. The majority of fungi identified belonged to Ascomycota and Basidiomycota, phyla that are dominated by saprotrophs. In conclusion, our findings shed light on the fungal communities associated with Armadillidium species, providing valuable insight into the biology of terrestrial isopods.