Armillaria is a genus of root infecting basidiomycetes, which includes nine North American biological species. Anonymous nucleotide sequences obtained from four different primer pairs were combined to produce a data set which was analyzed phylogenetically. The data indicated that randomly chosen sequences from the genome were capable of resolving the phylogenetic history of species of Armillaria and provided strong support for intraspecies clustering. NABS III and VII formed a significant monophyletic clade, with III being derived from the more broadly distributed NABS VII. Sequences of isolates of NABS V showed a high degree of variation. This variation may be an indication of recent sympatric speciation, with NABS IX and X diverging from a genetically diverse NABS V. NABS I formed a monophyletic clade despite the variation in geographic distance among the isolates. The position of NABS II as ancestral to NABS I was discussed. However, literature evidence favored divergence of NABS II from NABS I, while this study illustrated genetic similarity of NABS II with NABS VI. NABS VI was the most divergent of the North American species and represented the outgroup. A molecular clock of NABS Armillaria was proposed.