The morphological variation of basidiomata of Filoboletus manipularis (Berk) Singer collected in southern Viet Nam was studied. Phylogenetic analyses comprising three gene loci indicated that these collections, although exhibiting widely varying morphologies, represented a single species with a population composed of genetically diverse, sexually compatible monokaryon parental strains. No correlation was found between any aspect of morphological variation and intraspecific phylogenetic patterns for the three gene loci studied. Primers were designed to amplify the intron-rich 5′ region of the translation elongation factor 1-α gene (tef1α) and amplicons cloned and sequenced to characterize the parental haplotypes for individual basidiomata. The presence of recombination over the entire morphological diversity seen was confirmed by split decomposition analysis and analysis of gene diversity indicated a lack of allelic fixation within local populations. On several occasions, more than two apparent parental haplotypes were characterized from individual basidiomata, indicating that at least some basidiomata are chimeric or otherwise develop from a multinucleate condition. The literature supporting our observations of the occurrence of multinucleate basidiomata is reviewed and possible mechanisms for this phenomenon are proposed.