Display omitted •Recent progress in analysis of fermented foods microbiota is reviewed.•Fermentation is facilitated by microorganisms or complex microbial communities.•These microbes function as starter, adjunct or probiotic strains.•Strains isolated from fermented milks can be employed as therapeutic adjuvants.•Traditional and, increasingly, omics-based approaches are used to determine microbial composition and functionality. Fermentation is a traditional approach to food preservation that, in addition to improving food safety, also confers enhanced organoleptic, nutritional, and health-promoting attributes upon those foods. Dairy products can be fermented by a diverse microbiota. The accompanying microbes can be studied using a variety of different, including ‘omics’-based, approaches that can reveal their composition and functionality. These methods have increasingly been recently applied to study fermented dairy foods from the perspective of genetic diversity, functionality and succession. The insights provided by these studies are summarised in this review.