We surveyed species composition in relation to substrates, and microsite characteristics of temperate conifer species in an old growth Chamaecyparis obtusa forest on Mt. Shiraga, Kochi, Japan. We established nine study quadrates on a gentle slope where masses of rock or dwarf bamboos are dominant on forest floor, and we measured the diameter at breast height of all trees that were more than 1.5 m in height and the height of all conifer seedlings (< 1.5 m in height) while recording their standing substrates: stump, fallen log, rock, mound, and ground. According to detrended correspondence analysis, the nine quadrates were roughly divided into a group dominated by Chamaecyparis obtusa and Tsuga sieboldii, and a group of mixed broad-leaved tree stands, implying that the former establish on a block slope and the later establish on the ground. Chamaecyparis obtusa seedlings significantly established on fallen logs and old stumps while larger trees (> 1.5 m in height) were found on stumps. Thirty percent of large Chamaecyparis obtuse trees were established at an elevated position above the ground, and half of them had stilt-like roots. Tsuga sieboldii seedlings were established on rocks and stumps, while the larger trees were found on stumps. Both seedlings and larger trees of Pinus parviflora established on stumps though there were few of these. Abies firma seedlings were more likely to be found on the ground, but intermediate-sized trees were missing, showing their limited regeneration. Thus the stumps and logs play an important role as microsites for establishing conifers, except Abies firma, in an environment in which masses of rock or dwarf bamboo are dominant on the forest floor.