To quantify the species composition of epiphytic woody plant communities in the canopy, we climbed trees using ropes and directly measured the epiphytic woody plant communities on a Cryptomeria japonica tree that regenerated after harvesting in Edo Period and a remnant tree left standing in a mixed coniferbroadleaf forest on Yakushima Island. We found only 4 species and 8 individuals on the regenerated tree, whereas we found 12 species and 391 individuals on the remnant tree. In the remnant tree, Sorbus commixta occurred in the upper canopy, while Vaccinium yakishimense occurred in the mid to lower canopy and Rhododendron tashiroi occurred on the lower stem, reflecting vertical stratification among species. Based on their size distribution, we inferred that the dominant epiphytes are regenerating in the canopy. Our results suggest that remnant trees function as refugia for species that do not occur on the ground and that retention of large, old trees after harvesting contributes to maintaining biodiversity of the forest.