The present invention relates to the improved process for the preparation of highly pure form of S-[l,2-(dicarbethoxy)-ethyl]O,O-dimethyl phosphorodithioate having formula (I). The compound of formula (I) has adopted name "Malathion". The present invention also relates to the novel process of preparing intermediate O,O-dimethyldithiophosphoric acid of formula (II), which is useful in the preparation of Malathion. The Malathion prepared by the process of this invention is highly storage stable and toxic impurities are much lower than any other commercial preparation available for the pharmaceutical purpose.