Beer has been generally recognized as a microbiologically stable beverage. However, deviations in the brewing process may occur due to the activity of lactic acid bacteria (LAB). The growth of LAB during the brewing process implies a competition for nutrients with yeasts, causing decreased ethanol yields. Moreover, quality degradation caused by LAB spoilage can be observed due to the production of off-flavors (high indications of diacetyl and lactic acid), changes in color and excessive turbidity. This study aims at the microbiological investigation of non-pasteurized beer products, before and after filtration, as well as the detection and molecular identification of these threats. Sampling was performed at selected points of a beer production line on industrial scale to determine the population of Total Viable Count, yeasts and LAB. The samples are classified in the "Lager" category, fermented using strains of Saccharomyces pastorianus. The sampling points included the pre- and post- filtration step, the buffer line, the filling tank, the packaged but non-pasteurized product and the packaged pasteurized product to confirm the effectiveness of heat treatment. Samples were collected in two different batch productions. The results showed that the population of LAB was relatively low. Before filtration, levels were 1.52 log CFU / mL and 3.44 log CFU / mL in the first and second batch respectively. Absence of LAB (<1.0 log CFU / mL) was observed afterwards in all sampling points. A total of 86 LAB colonies were isolated and subjected to molecular analysis to characterize the biodiversity of this microbial group. The molecular technique applied was rep-PCR using the GTG5 as primer. The detection of the rep-PCR products was undertaken by the PFGE technique, followed by grouping of the strains using the Bionumerics software and finally selecting 20 representative isolates for sequencing.