In recent years, microbes are exploited significantly for the production of industrially useful enzymes. Microbial pectinase types play a vital role in clarification of fruit juice and it accounts for one-third of global food processing industrial sector. In this research work, the potential isolates which includes bacteria and actinomycetes were screened for the polygalacturonase activity from soil samples of fruit industrial dumps as it was enriched with mango, papaya, guava etc. fruit industrial waste for more than 30 years. The screening of potential pectinolytic bacteria and actinomycetes was carried out by using selective media enrichment techniques. The biochemical and molecular characterization were carried out for the potential isolates. Further, the crude pectinase was partially purified by using ammonium sulfate precipitation, column and DEAE sephadex chromatography. The specific activities of partially purified enzyme from potential microbes were enhanced up to two-fold of about 2438 and 633U/mg of protein respectively. The molecular weights of the enzyme from Bacillus and Actinomycetes were determined as 34.9 and 45.1 kDa by SDS-PAGE.