The present study was aimed at the development of a somoclonal variant and isozyme marker for Phyllanthus amarus Schum & Thonn using inter-nodal segments and the enzyme peroxidase. Maximum callus proliferation was obtained on Murashige and Skoog’s medium supplemented (MS) with 1.0 mg/l of 2,4-Dichlorophenoxyacetic acid. Three weeks-old pale yellowish white semi-friable callus was used for organogenesis; the maximum percentage of multiple shoot formation (85%) was achieved after 4 weeks when callus was cultured on Murashige and Skoog’s medium fortified with 1.0 mg/l of 6-Benzylaminopurine.The multiple shootlet formations were also achieved in the presence of the same concentration. The maximum formation of rootlets was observed on MS medium augmented with 1.0 mg/l of Kinetin and 0.5 mg/l of Naphthalene acetic acid. The banding pattern and phytochemical constituent differences were observed between mother plants, directly regenerated via nodal segments, calli, and calli mediated plants. The calli mediated somoclonal variation was confirmed through isozyme (peroxidase) and phytochemical analysis. The isoperoxidase banding profile showed a difference in calli and calli mediated plants. The phytochemical study confirmed the presence of more alkaloids, saponins, tannins and others from calli and calli mediated shoots and roots. Hence the isozyme banding patterns can be used as molecular markers in future plant breedings or genetic improvement programmes.