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The D1/D2 regions of the large subunit (LSU) rRNA genes of 65 strains of Monascus and Xeromyces were PCR amplified and sequenced in both directions. Maximum-parsimony analysis produced five most parsimonious trees. The strict consensus tree of these five parsimonious trees clustered M. eremophilus, M. ruber, M. pilosus, M. purpureus, and M. sanguineus in the same clade, reflecting high sequence similarity. M. sanguineus, M. purpureus, M. ruber, and M. pilosus differed in one or two nucleotides. The sequence of M. eremophilus ATCC 62925 isolated from a xerophilic environment differed from M. purpureus in only one nucleotide, despite pronounced morphological and ecological differences when compared with the other species. M. lunisporas, M. floridanus, M. pallens, and X. bisporus were each placed in a separate branch, confirming their taxonomic descriptions as individual species.Maximum-likelihood analysis on the same data set generated a single tree and grouped the species of the first clade in the parsimony analysis into a single clade but placed the rest of the Monascus species and Xeromyces bisporus on different branches. The trees inferred from both analyses revealed a monophyletic relationship between Monascus and Xeromyces, when compared with other related cleistothecial or imperfect genera.