Abstract. Heterokaryotic isolates from decay and single basidiospore strains of the American pine form of Heterobasidion annosum were collected from a 70 X 60 m plot in a relatively undisturbed red pine-white pine stand in New Hampshire. Fourteen somatic incompatibility groups (SIG) were detected among the 24 heterokaryons obtained from 23 pine trees and stumps. Most of the red pine mortality was due to annosum root rot, which occurred in two pockets. The eight diseased trees at the south end of the plot were colonized by one SIG, and eight diseased trees at the north end of the plot were colonized by six SIGs. Seven other SIGs were identified from individual stumps. Most SIGs had unique mating type alleles and isozyme patterns, and all had unique DNA fingerprints (PstI digestions probed with (CAT)5). All heterokaryons of a given SIG had identical isozyme alleles at each of four tested loci, identical DNA fingerprints, and identical mitochondrial (mt) DNA polymorphisms (digestion of total DNA with HaeIII, MspI or CfoI and ethidium bromide staining). SIGs at the north end of the plot had similar DNA fingerprints, isozyme markers and mtDNA profiles. One explanation for the relatedness of adjacent clones is that dikaryons of H. annosum are not stable and interact with other neighboring heterokaryons and homokaryons.