The transition to terrestrial environments has occurred repeatedly and at different geological times in arthropods, but almost no information is available about the role of symbiotic microbiota in such process. Here we investigated the associated microbiota of a terrestrial brachyuran crab, Chiromantes haematocheir, using a targeted metagenomic approach. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. We found stable and organ-specific communities of microorganisms associated to the gut and the gills of the crabs, the former involved in the digestion of vascular plant tissues. These communities were mainly composed by prokaryotic organisms and significantly differed from the fungi-dominated ones present in the environment. Our results suggest that the establishment of a specific, stable -microbiota may be crucial to drive evolutionary transitions, as colonization of terrestrial environments.