The clonal structure of Perenniporia subacida, a wood-rotting basidiomycete, was studied in a 30-year-old stand (site A; 1 ha) and a 43-year-old stand (site B; 0.5 ha) of Chamaecyparis obtusa in northern Kagawa Prefecture, Japan. A total of 110 isolates from decayed trees, stumps, wooden fences, logs, and mycelial mats were analyzed by amplified fragment length polymorphism (AFLP) and somatic incompatibility test (SIT). The results of AFLP, which agreed with those of SIT, revealed that the P. subacida population consisted of at least 17 genets at site A and 6 genets at site B. Individual genets were found in 1 to 9 trees at site A and in 1 to 7 trees at site B. One particular genet had spread over a distance of 70 m. Root contacts were observed among roots of decaying stumps and living trees at both sites. White mycelial mats were often found where roots made contact between stumps and neighboring trees. These results suggest that P. subacida spreads vegetatively over significant distances through root contacts.