This study hypothesized that geographic segregation of certain extreme natures of the same kind could be an indicator of access to new natural microbial resources. Root-layer fungi and soil properties native to well-conserved volcanic topographies from two geographically segregated ocean volcanic islands beside the Korean Peninsula were analyzed. Four segregated sampling sites that represented the ocean volcanoes’ unique natural characters (tuff layer, caldera, and two steep cliffs) were examined. A total of 1356 operational taxonomic units classified into 7 phyla and 196 genera were obtained. Soil analysis showed that the sand proportion varied from 32.0–57.4%, and silt, 39.4–64.8%. The tuff layer terrain was the only terrain classified as silt soil. Soil Corg contents ranged from 2.78–15.12%; TN, 0.159–0.843; salinity, 0.001–0.019; and pH, 5.0–7.4. The larger the island area, the less oceanic salinity inflow, but TN and Corg decreased, and pH increased. The Shannon diversity index varied from 4.81–5.23 and was higher at the larger or center of larger islands. As geographic segregation (distance) increased, the proportion of taxa commonly identified decreased. Thus, geographic isolation of certain natural features (e.g., volcanic islands) may be a preferential clue to accessing a broader range of potential microbial resources.