The present study was carried out for determination of the microbial pigments present in the combination of Citrus reticulata (peel) and Carica papaya are the medicinally important plants belonging to the Rutaceae & Caricaceae family respectively. In the present study, the extract of Citrus reticulata peel with Carica papaya pulp has been subjected to fermentation by using Penicillium purpurogenum and analyzed by analytical techniques. This analysis revealed that microbial extract of Citrus reticulata and Carica papaya contains 1,3-Butanediol, (S)-, 1,3 Propanediol, 2-Butanone, 3-Hydroxy, 2-Octanol, Benzofuran, 2,3-Dihydro, 2-Methoxy-4-Vinylphenol, 3-Methyl-1,6-Heptadien-3-Ol, Decanoic Acid, Ethyl Ester, 4-Hydroxy-3,5,5-Trimethyl-4-[(1e)-3-Oxo-1-Butenyl]-2-Cyclohexen-1-One, 8-Hydroxy-2h-Chromen-2-One, Hexadecanoic Acid, and Beta-Sitosterol.