The aim of this work was to identify the main microbiota in raw cow milk from dairy farm of Slovakia and to describe the selected microorganisms responsible for thermostable protease and lipase production which can affected the quality of dairy products. The main bacterial classes identifying by MALDI-TOF MS were Gammaproteobacteria (62 %), Actinobacteria (19 %) and Bacilli (12 %). The dominant microbial genus of raw cow milk was Pseudomonas. From milk bacteria, the strain Lactococcus lactis and from the family Enterobacteriaceae, namely Enterococcus faecalis, Hafnia alvei, Citrobacter braakii and Raoultella ornithinolytica were observed in raw milk. The spoilage of milk products is caused by thermostable enzymes with lipolytic and proteolytic activity. Qualitative proteolytic and lipolytic activities were performed on skin milk agar and olive oil, respectively. From 16 identified microorganisms, only 8 strains (P. fragii, P. gessardii, P. lundesis, H. alvei, C. braakii, R. ornithinolytica, Kocuria rhizophila and Candida inconspicua) showed protease activity. Quantitative protease and lipase activities were determined by casein and olive oil, respectively. The highest both activities were measured for the genus Pseudomonas. While lipases produced by all isolated microbial species lose enzymatic activity at 77 °C for 30 – 40 min, almost proteases showed comparable activities during whole pasteurization experiment at selected experimental conditions (70 °C, 40 min).