Mushrooms that are morphologically indistinguishable from Russula virescens (Schaeff.) Fr. are among the most popular wild edible mushrooms in Yunnan province, southwestern China. However, almost nothing is known about their biology. This study investigated the diversity and population genetics of a R. virescens ally from Yunnan. A total of 210 samples were collected from 13 geographical locations throughout the main distribution range in Yunnan. The patterns of genetic variation within and among these geographic populations were analyzed using sequences from three nuclear and two mitochondrial DNA fragments. Analysis of the ITS sequences revealed that samples from Yunnan showed 3-6% sequence difference from R. virescens samples from North America and Europe and formed a distinct clade. Our multilocus population genetic analyses suggested frequent gene flow among geographic populations of the R. virescens ally in Yunnan. Interestingly, the nuclear and mitochondrial genes exhibited different levels of gene flow and recombination. We discuss the implications of our results for understanding speciation, reproduction and conservation of this important biological resource.