In this brief, the authors explore and review the current knowledge regarding the role of molybdenum in the evolution of biological systems and their interaction with biogeochemical cycles. Special emphasis is placed on biological nitrogen fixation and the nitrogen element cycle. The origin and evolution of molybdenum cofactor biosynthetic pathways as well as the evolutionary significance of molybdenum containing enzymes appearance is analyzed. Original data regarding nitrogen fixation pathways and related enzymes molecular evolution processes is presented. The trace element molybdenum is essential for nearly all organisms and forms the catalytic center of a large variety of enzymes such as nitrogenase, nitrate reductases, sulphite oxidase and xanthine oxidoreductases.