The diversity and role of the gut microbiota of insects is a rapidly growing field of entomology, primarily fueled by new metagenomic techniques. Whereas endosymbionts in the guts of xylophagous or herbivorous insects are well studied, the microbiomes in moss-eating (bryophagous) insects remain uncharacterized. Using the Illumina MiSeq platform, we determined the composition of microbiomes in the gut, abdomen and on the body surface of two bryophagous species: Simplocaria semistriata (Fabricius, 1794) and Curimopsis paleata (Erichson, 1846) (Coleoptera: Byrrhidae). Gut microbiomes differed substantially from abdominal microbiomes in the same individuals, which indicates the need to separate them during dissection. Microbiomes in the gut and abdomen differed markedly from surface microbial assemblages. Gut microbiomes in bryophages had the highest MOTU richness, diversity and relative rarity. The eudominant bacteria in the guts and abdomens of bryophages were Novosphingobium, Bradyrhizobium, Ralstonia and Caulobacter, which are responsible for the detoxification of secondary metabolites or nitrogen fixation. These are less common in the surface samples and, therefore, likely to be associated with the specific ability of bryophages to feed on mosses.