In order to preserve the specificity of artisanal cheese and to minimize variations in quality, real-time PCR can be applied to monitor the dynamics of autochthonous bacterial population throughout ripening. This may give the basis for the selection of species and strains that can be used to deliver safe products with balanced texture and flavour, and moreover, it can be applied to monitor the abundance of slow-growing or nonculturable species. The aim of this study is to evaluate the application of real-time PCR and plate count analysis in order to follow the dynamics of lactic acid bacteria (LAB) and enterobacteria during the ripening of traditional Istrian cheese. The abundance of all LAB was increased by prolonging the ripening time and reached the plateau after 90 days. The present study demonstrated that Lactococcus counts were closest to total bacterial count irrespective of the applied method, confirming Lactococcus spp. as one of the dominant bacterial groups associated with the ripening of Istrian cheese. Enterobacteria were mainly present at early phases of cheese ripening, whereas at later time a decrease was visible in samples from all farms.