Abstract: High-throughput sequencing was used to study the microbial diversity of suan yu which were sample from six locations of southeastern Guizhou. The results showed that the microbial community of suan yu were complex and quite different among samples. The content indexes showed significant difference also in the lactic acid,protein and fat.The pH of suan yu from Jianhe was highest,the content of lactic of Tianzhu suan yu was dozens of times as much as others.Analysis of microbial community structure of suan yu showed that,the predominant bacteria and fungi of suan yu in six counties were Firmicutes and Ascomycota at the phylum level. At the genus level,Lactobacillus was the predominant bacteria of suan yu for Jianhe county,Rongjiang county,Tianzhu county,Congjiang county and Tetragenococcus was the predominant bacteria of suan yu for Jinping county and Liping county. At the genus level,the predominant fungi of suan yu in Jianhe county,Jinping county,Liping county,Rongjiang county,Congjiang county was Zygosaccharomyces and the predominant fungi in Tianzhu county was Kazachstania. The Heatmap of microbial community revealed that the dominant bacteria and fungi of suan yu in Jianhe,Jinping,Liping and Rongjiang were most similar in composition. Canonical conespondence analysis indicated that lactic acid might be the most important factor influencing the dominant bacterial and fungal community. The results of this study have provided a theoretical basis for the industrialization of traditional fermented fish in Guizhou.