This paper reviewed the new techniques of molecular microbial ecology,which included two kinds of methods,and one was non-based on genomic DNA,including sole carbon source utilization patterns(SCSUP) and phospholipids fatty acid patterns(PLFA);the other was based on genomic DNA,including clone library analysis,metagenomics library analysis,guanine+cytosine(G+C) content analysis,total DNA re-association,community level-DNA cross hybridization,fluorescence in situ hybridization(FISH),DNA micro-array,denaturing/temperature gradient gel electrophoresis(DGGE/TGGE),single-stranded conformational polymorphisms(SSCP),restriction fragment length polymorphism(RFLP)/amplified ribosomal DNA restriction analysis(ARDRA),terminal restriction fragment length polymorphism(T-RFLP),ribosomal intergenic spacer analysis(RISA),randomly amplified polymorphic DNA(RAPD),and so on.Their potential applications in food industry were summarized: discovery of new strains,producing new enzymes,improving new techniques,and keeping food quality and safety.It provides new technical supports for deeper development of food industry.