Abstract. Decrease in species diversity by overgrazing is one of the crucial indicators for ecosystem deterioration. Sika deer (Cervus nippon Tamminck) has grazed various plants on Nakajima Island, Hokkaido, Japan, for a few decades, due to low food availability. We examined if diverse microtopography supported high species diversity by conserving specific plants on the grassland of the island where overgrazing by deer occurred. Based on TWINSPAN analysis, three plant community types were classified: grasslands represented by short seed plants, ferns, and unpalatable forbs. Grasslands dominated by short and/or unpalatable seed plants established on the flat ground, while fern species except Equisetum arvense did not establish there. Soil hardiness was higher on short-plant grasslands than on unpalatable-forb grasslands, suggesting that palatability on plants was related to plant community differentiation on the flat ground. Of 10 fern species recorded, 9 species established mostly in deep pits. Pit depth was more important than pit area to maintain high fern diversity. Those results indicated that diverse microtopography, i.e., pit development, supports fern diversity, because of the multiplier effects of predator avoidance and preferable sites for fern establishment. Diverse and/or specific microtopography must be a prerequisite to conserve rare species and high diversity in such disturbed areas.