Microbial communities in food and food production establishments have highly versatile structures based on various extrinsic factors. The information gained by large-scale microbial community analysis not only can deepen the understanding of food microbiology in general but also can lead to improvement of food production systems for increased quality and safety and extension of shelf life. This chapter reviews the most recent methods applied to microbial communities, and presents examples of some cutting-edge technologies. Molecular methods have been developing rapidly in recent years both for specific detection of single species and for screening assays that allow the species composition of a given food sample to be unraveled. Examples of those methods are 16S rRNA clone analysis, fingerprinting methods such as terminal restriction fragment length polymorphism (t-RFLP) and denaturing gradient gel electrophoresis (DGGE), tag-encoded pyrosequencing, single-nucleotide primer extension (SNuPE), and microarrays. Furthermore, flow cytometry is also addressed in the chapter, but this technique is based on single-cell analysis whereby a cell suspension is concentrated by nanofluidics and analyzed by laser technology. High-throughput analysis of microbial populations in food products and food processing environments has revealed the existence of a higher complexity in the microbial world than previously expected. The new approaches provide opportunities for further understanding of the microbial developments that are initiated during food production and storage.