Abstract: This study highlights the key role of peroxidases influencing somatic cells towards embryogenic pathway. Further the clonal identity of somatic seedlings was assessed using RAPD and ISSR markers. The lowest peroxidase activity was observed in embryogenic cultures on maintenance medium showing elongated cells with cleavage polyembryony as compared to control. Highest peroxidase activity was observed in non-embryogenic cultures showing round, globular and oval cells. Peroxidase activity is not only involved in reducing the accumulation of toxic amounts of H2O2 but might also influences the conversion of somatic cells into an embryogenic state and, therefore, can be used as a biochemical marker to differentiate embryogenic and non-embryogenic cultures. RAPD and ISSR analysis found no evidence of genetic variation either within or between the embryogenic lines established from three of these trees, or between these lines and the trees of origin, or between somatic embryos derived plantlets and the trees of origin.