Background: Tardigrades are microscopic invertebrates that can withstand complete desiccation, but their inter-species interactions within their microhabitat encompassing prokaryotes and eukaryotes remains relatively unexplored. Here I utilized a combined meta-barcoding of eukaryotes and prokaryotes, to simultaneously identify the entire community structures within xeric and mesic mosses that harbor tardigrades.</p><p>Results: Population of organisms within the microecosystem was successfully determined in 45 xeric moss samples and 47 mesic moss samples. Organismal composition was largely consistent regardless of the moss/lichen substrate, but were significantly affected by the environmental humidity. Xeric mosses containing xerophilic tardigrades and other anhydrobiotic invertebrates tended to have significantly limited biological diversity, suggesting strong selection due to the extreme desiccation.</p><p>Conclusions: Combined meta-barcoding approach to capture both the eukaryotes and prokaryotes can successfully elucidate the community structures within microscopic ecosystems, and this can be a potential approach in the study of microecology for meiofauna including tardigrades.