Detoxification of pesticides through biological means is receiving serious attention as an alternative to existing methods. In this perspective molecular and phylogenetic analysis of fungal strain FS 1 identified as Aspergillus oryzae was isolated and selected for the present study. In vitro biodegradation of endosulfan under agitating conditions was comparatively more than that under stationary conditions. TLC and HPLC analysis revealed the formation of various intermediates of endosulfan metabolism including endosulfan diol, endosulfan lactone and endosulfan ether. Interestingly, endosulfan sulfate; a persistent and toxic metabolite was not detected indicating complete mineralization of endosulfan. The results of this study suggest that the isolated strain could be a valuable source of potent endosulfan-degrading enzymes for use in bioremediation.