Genetic variation within a collection of 25 isolates of Monascus from red rice and sofu was assessed with RAPD markers using
genetic distances (1-Jaccard's coefficient) calculated for all combinations of isolates. Cluster analysis based on genetic distance was
performed using the Ward's minimum variance method. Five distinct clusters were revealed based on genetic distances between and
among clusters. The robustness (reproducibility) of the cluster assignments was tested by resampling (bootstrap) analysis. Cluster
distribution was visualized as a three-dimensional graph based on multiple correspondence analysis. A dendrogram, based on the
clusters, was constructed to examine the relationships. Three clusters accounted for 21 isolates; the fourth cluster consisted of three
isolates which were quite distinct from each other and all other isolates. The fifth cluster, a single isolate from Japan, was very
different from all others in RAPD patterns and was used as an outgroup. Resampling analysis indicated that the 25 isolates
represented four genetic lineages of red rice fungi, suggesting that a relatively narrow genetic source of Monascus isolates is used in
food products in Asia.