We conducted line route censuses of fungal fruiting bodies from August to September in 2005 and 2006 along ridges and valleys and compared the differences in the encounter rates of fungal fruiting bodies (= fruiting bodies seen per census kilometer) between types of topography and between fungal functional groups (i.e., ectomycorrhizal and saprobic fungi) in warm temperate evergreen broad-leaved forests on Yakushima Island, Japan. We found 251 fungal fruiting bodies (26 families, 50 genera, and 65 species) in total, including 51 bodies from Tricholomataceae, 41 from Russulaceae, 25 from Boletaceae, and 19 from Amanitaceae. The encounter rate of ectomycorrhizal fungi was greater at the ridge route (26.7 unit/km) than at the valley route (8.7 unit/km) and that of saprobic fungi was greater at the valley route (25.0 unit/km) than at the ridge route (12.5 unit/km). In addition, we conducted 7-year intermittent sampling and identifi ed 40 families, 96 genera, and 142 species. The topography-specifi c emergence pattern of the intermittent sampling method was similar to that of the line census method. The fungal species composition in this study was possibly affected by a topographic gradient for both fungal functional groups through soil moisture, nutrient availability, and host tree distribution.