Background Strains of yeast have been analyzed from vineyards, wineries and forest in Europe, North America, South America, South Africa, Asia and Australia. However, the genetical diversity of natural population of Saccharomyces bayanus in Southwest of China has not been studied yet. [Methods] The sequences of ITS, HIS3, SSU1 and MET2 genes, microsatellites analysis and AFLP analysis were used to access the genetic diversity of the S. Bayanus isolated from vineyards in Shangri-la, Yunnan, China. [Results] Our sequences of ITS, HIS3, SSU1 and MET2 genes come from vineyard S. bayanus in Shangri-la, Yunnan, China, which are quite similar to a Europe strain CBS7001, and they look to be derived from Europe. There were only 3 SNPs among the isolates. Microsatellites analysis results illustrated that all isolates appeared to belong to families of closely related genotypes. Seven colonies obtained from two different vineyards from Deqin County (three from Chizhong, and four more from Liutongjiang) all had genotypes that are very similar to a winery-derived strain 7A6 from New Zealand. The polymorphism level of AFLP analysis is much more than of the microsatellite. The results of AFLP analysis indicated that 63.72% of the variation was found among the different geographic origin isolates, while 36.28% was found among the same geographic origin ones. [Conclusion] Both microsatellites and AFLP analysis results showed that genetic diversity among these isolates was quite low, and S. bayanus populations were geographically partitioned generally.
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