The microbial diversity of artisanal Livanjski cheese from traditional farms and dairies was analysed. The polyphasic approach included the isolation of microorganisms by using culture-dependent methods and the identification of viable isolates by sequencing methods. In total, 159 isolates were identified, including five strains of yeast and 15 strains of fungi. Twenty-two species of homofermentative and heterofermentative lactic acid bacteria were classified. The Shannon-Wiener index of diversity ranged from 0.462 to 2.51 within the cheese samples from the farms and dairies. The hygiene conditions during cheese production and the age of the cheese significantly influenced the counts and diversity of microorganisms.