A differential pattern of peroxidase (E.C. 1.1.11.7) has been observed in reciprocal F1 hybrids of Eucalyptus (FRI-4 and FRI-5) produced using parental combination of E. tereticornis and E. camaldulensis. The hybrids were characterized for the qualitative, kinetic parameters (total and specific activity, units, Km and Vmax) and partial purification of peroxidase. The qualitative study showed the presence of high molecular weight peroxidase isoforms i.e. 260 KD, 250 KD and 110KD bands. A strong maternal inheritance was observed for 260 KD loci in FRI-5. Kinetic characterization of peroxidase revealed that F1 genotypes had efficient peroxidase system over their parental combination resulting in 8 -10 times more heterotic vigour. The FRI-5 genotypes were found to be having efficient peroxidase system with lowest Km values (0.12mM-0.17mM) and higher Vmax values ranging from 0.07-0.14mM min-1mg prot-1. The study revealed the role of maternal inheritance and was found that better genotypes are produced when superior parents are used as seed parent. The results suggest the efficient use of peroxidase marker for the identification of the better genotypes in forest tree species.