A filamentous fungus, Aspergillus niger, has tremendous agricultural and industrial importance and was used by many researchers for the production of industrially important enzymes. Many Aspergilli were recognized as both human pathogenic and mycotoxin producers too. Even though various Aspergillus species have been used widely in research, their taxonomy is unclear due to very close morphological features among their species. In the present study, different Aspergillus niger strains were isolated from the decayed fruits and vegetables, and the enzyme profiling for the production of industrially important enzymes like amylase, pectinase, lipase, cellulase, catalase, and urease enzymes was done. Among four different strains isolated, strain number RSS01 was producing, a high yield of pectinase, and on molecular identification, it has been identified as Aspergillus niger strain RA401 and submitted to Genbank bearing an accession number MN153032. Hence this local strain can be used in the large-scale production of Pectinase enzymes.