Kefir is a traditional fermented milk associated with several health benefits, such as immune system modulation, as well as antimicrobial, antitumor and antioxidant activity. The aim of the current study was to investigate the microbial dynamics of kefir production based on high‐throughput DNA sequencing. Results of sequence analysis have grouped the reads into 303 and 112 amplicon sequence variants (ASV) for bacteria and fungi, respectively. Firmicutes, Bacteroidetes and Proteobacteria were the prevalent bacterial phyla, whereas Lactococcus was the prevalent bacterial genus. Ascomycota was the main fungal phylum. Data have shown heterogeneity in diversity and abundance distributions between milk kefir samples.