The aim of this work was to perform the screening of microorganisms, previously isolated from samples of agro-industrial waste and belonging to the culture collection of our laboratory, able to produce polygalacturonases (PG). A total of 107 microorganisms, 92 newly isolated and 15 pre-identified, were selected as potential producers of enzymes with PG activity. From these microorganisms, 20 strains were able to synthesize PG with activities above 3 U mL. After the kinetic study, the enzyme activity was increased up to 13 times and the microorganism identified as Aspergillus niger ATCC 9642 and the newly isolated W23, W43, and D2 ( Penicillium sp.) after 24 h of fermentation led to PG activities of 30, 41, 43, and 45 U mL, respectively. The RAPD analysis demonstrated that the selected strains differs genetically, indicating that no duplication of strains among them in the experiments for polygalacturonases production was verified.