Abstract: In order to explore the relationship of microorganisms between meju and soybean paste,two natural fermented meju and one industrial fermented meju were taken as objects,MiSeq sequencing technology was used to analyze microbial diversity of three different meju and its fermented soybean paste. The results showed that the dominant microorganisms in phyla were Ascomycota and Firmicutes;At the level of genus,dominant fungi in samples are Penicillium and Mucor,however,the composition of bacteria in different samples were different,the dominant genus of LK and SK were Bacillus and Lactobacillus,while the dominant genus of FK were Lactobacillus,Bacillus subtilis and Lactobacillus brevis;In the late stage of fermentation,although different samples have different community composition of bacterial at the initial stage of fermentation,as the fermentation progresses,the dominant bacteria was Tetragenococcus. This study clarified the microbial relationshipbetween meju and soybean paste,which provided a theoretical foundation for controlling the fermentation process of soybean paste.