One hundred thirty-five single-spore isolates were collected from grape vineyards from 15 provinces or autonomous regions belonging to five viticulture climatic zones in China. All the isolates were identified as Botrytis cinerea based on their morphological and molecular characters. The 135 isolates were all heterothallic isolates. Seventy-one isolates belonged to the MAT1-1 type and 64 were characterized to MAT1-2 type. All the isolates studied belonged to Group II based on PCR-RFLP of the Bc-hch locus. The four TE genotypes, transposa, Boty-only, Flipper-only, and vacuma, comprised 51.9%, 33.3%, 10.4%, and 4.5%, respectively, of the total population. The frequency of transposa was highest in the total population and the most of any subpopulation (each viticulture climatic zone), and Boty-only was highest in warm areas (46.2%). Vacuma was mainly distributed in northern China, although in small amounts, and Flipper-only was mainly was distributed in humid tropical areas (42.9%). A microsatellite analysis of B. cinerea populations was performed to assess the genetic population structure. A total of 127 different MLGs were identified among 135 B. cinerea isolates, with a genotypic diversity of 0.9991. The transposa population isolates showed higher genetic diversity than other populations. Pairwise tests of genetic differentiation among four TE-type populations yielded generally low to high Gst values. All isolates belonged to two genetic clusters. The population microsatellite diversity and genetic structure had a certain correlation with the TE type and geographic origin. This is the first report of the genotypic diversity of B. cinerea isolates from grape vineyards across China.