The chemical characteristics of kefir cheese produced by different types of milk was investigated. There are not any residual alcoholic in kefir cheese produced from different kinds of milk. Total solids, total nitrogen, and protein, fat as well as fat/dry matter values were high in kefir cheese produced from buffalo milk in comparison with the kefir cheese produced from cow and goat milk. The use of buffalo milk for production of kefir cheese affected the preferences of the tasters. And gained the tasters’ preference compared to the other kefir cheeses. All samples of kefir cheese were free from Coliform group and staphylococcus spp and yeasts. The microbial community composition of kefir grains was also investigated by culture-independent methods (PCR). The dominant microorganisms were Leuconostoc mesenteroides, Lactobacillus brevis, Lactobacillus plantarum, Lactococcus lactis, Kluyveromyces lactis, Streptococcus thermophilus, Saccharomyces cerevisiae, Pediococcus pentosaceus and Lactobacillus pentosus