Next generation sequencing technology has revolutionized studies in fermentation process, in particular, to explore the mechanism by which food microorganisms, including physiology, metabolic pathways, diversity and dynamic changes of microbial community. In addition, phylogenetic characteristics of different species or strains of the food microorganisms are disclosed. All these aspects will help explain how the microbes are interacting and responding to environmental factors. Bioinformatics analysis of genome and metagenome sequence data of food microorganisms could provide essential clues to improve fermentation process and function of microbes as well as control and prevention of foodborne disease outbreak. In this review, we summarized recent genomics and metagenomics studies on food microorganisms. The impact of next generation sequencing for the development and trends of food microorganism researches were discussed in details.