The genetic diversity of 169 blast fungus isolates collected from 44 susceptible rice varieties widely grown in 19 locations in Hunan Province was analyzed in 2010 by using 13 pairs of simple sequence repeat (SSR) markers. It was found that these isolates were classified into 8 genetic lineages at 0.8 similar levels, among which L01 was the dominant lineage and its isolates accounted for 66.86% of the total. Most genetic lineages contained isolates from several source areas and many rice varieties. The genetic relationships between the lineages and the source areas and between the lineages and the rice varieties were complex. The isolates from the same locations or from the same varieties had a relatively close genetic relationship, but the differentiation of the blast fungus physiological race varied in different locations. The genetic diversity of M. oryzae was related to the terrain and the number of rice varieties of a location. There was a greater genetic diversity of M. oryzae in mountainous regions with a high elevation than in hilly areas. The more rice varieties planted in a location was, the greater genetic diversity of M. oryzae was.