Pectinases are believed to become important industrial enzymes. These can be produced through different microorganism (bacteria and fungi) Pectinases are very important enzymes in food manufacturing industries. Pectinase shares the total enzyme production of about 25 % on global scale. The current study was focused on isolation and partial characterization of fungus that produces pectinase from orange peel. Samples collected from the fruit shop of Cantonment Lahore, Punjab. Samples collected from the fruit shop of Cantonment Lahore, Punjab. Total ten (10) isolates were identified from six (6) orange peel samples. Based on characterization on the selective growth media, the isolates were grouped as Aspergillus Niger. The isolates were further characterized by colony morphology, biochemical and molecular approaches. Four (4) strains were screened for pectinase activity out of which only one (1) harbor the pectinase. Quantitative determination of pectinase was carried out using DNS method using pectin as substrate. Microscopic, biochemical and molecular analysis indicated strains as Aspergillus Niger. A 565 amplified DNA confirmed the existence of Aspergillus Niger. The presently investigated indigenous A. Niger showed incredible potential for industrial use.