The current novel research work emphasis on the production and characterization of the pectin lyase (PL) and polygalacturonase (PG) from Bacillus cereus GS-2 by utilizing the agro-industrial pectin rich substrates i.e. orange, mango, apple, papaya peels. The morphological characterization of potential isolate was carried out with Scanning Electron Microscope (SEM) which shows the shape and morphology similar to Bacillus sp. Further, molecular identification was carried out using 16SrRNA sequencing and the sequence was successfully submitted in NCBI (GenBank) under the Accession No: KC571175. The characterization of pectic substrates i.e. fruit peels by Fourier Transform Infrared Spectroscopy (FTIR) revealed the presence of pectic acids, amine, carboxyl, carbonyl groups that assist in the pectinase enzyme production. Maximum pectin lyase and polygalacturonase activity of about12.66 U mL-1 and 11.00 U mL-1 was achieved utilizing an orange peel as major carbon source compared with other sources. Peptone and Urea acts as best nitrogen source for maximum PL and PG activity. The enzyme was partially purified by using ammonium sulphate precipitation, the pectinase activity (28.22 U mL-1). Further, it was purified by adopting novel technology like ion exchange chromatography, the yield significantly improved up to 2-fold (40.13 U mL-1) and it was later analyzed by SDS- PAGE and High performance Liquid Chromatography (HPLC), the size of pectinase was found to be 36Kda. HPLC results show a retention time of about (1.93 min) compared to control (2.518 min). This study has proven that agricultural waste like orange peels could be used as promising substrate for both pectin lyase and polygalacturonase production from novel Bacillus sp.