Abiotic environmental variables and invertebrate assemblages were compared among four habitat types (bare hollow, sphagnum-rich hollow, pool, and mat edge) on a floating mat in Mizorogaike Pond, Kyoto. We found differences in abiotic environments between two hollows and two inundated habitats (pool and mat edge); pH was significantly lower in hollow habitats than in inundated habitats, and water depths were significantly shallower in sphagnum-rich hollows than in inundated sites. The composition of invertebrate assemblages in the hollow was distinct from that in the inundated habitats. The abundances of some dominant invertebrate taxa or functional feeding groups on the floating mat differed between the hollows and inundated habitats, and were correlated with water temperature, pH and depth. These results indicate that habitat heterogeneity created by the coexistence of hollows and inundated habitats contributes to species diversity on the floating mat in Mizorogaike Pond. A comparison of the pH values in different wetlands revealed that both bog- and fen-specific components coexist within this system. In order to adequately manage and conserve peatland ecosystems, it is necessary to consider the importance and vulnerability of both hollows and inundated habitats in peatlands.