Biochemical marker is one of the important tools for the early identification and selection of somatic embryogenesis in plants. Studies in developing the biochemical marker for somatic embryogenesis of Eurycoma longifolia disclosed that the regenerated and non-regenerated cotyledons as well as embryogenic and non-embryogenic callus were significantly different in terms of the total protein content as well as the specific activity of peroxidase. The data obtained revealed that embryogenic tissue possess the highest amount of total soluble protein (64.24 mg/g fresh weight) and two protein bands (molecular weight = 25 and 21 kDa) were observed at high intensity. The highest specific activity of peroxidase ($578.1pm61.6;unit/mg$ soluble protein) was recorded in embryogenic callus and only $157.1pm20.5;unit/mg$ soluble protein was determined in the non-embryogenic callus. Results obtained also showed that there were variations in the peroxidase banding profiles of the four samples examined. Only two bands were observed in the non-embryogenic callus at the Rf of 0.24 and 0.27, whereas in the embryogenic callus, four bands with high intensity were detected at the Rf of 0.24, 0.41, 0.49 and 0.81.