An efficient in vitro micropropagation system for Erythrina variegata, a multipurpose tree legume was orchestrated as a tool for evaluating the effect of cobalt on morphogenesis and physiological processes of the plant. Various factors effecting in vitro growth and development were optimized. Among all the different concentrations and combinations evaluated, combination of 5.0 lM 6-benzylaminopurine (BA) and 0.5 lM 1-naphthaleneacetic acid (NAA) supplemented to MS medium induced maximum number (12.9) of shoots per explant with greatest (4.8 cm) average shoot length in 93.6 % cultures. Augmentation of cobalt at lower concentration (50 lM) to the optimized media significantly enhanced the growth parameters (shoot number and shoot length) and chlorophyll content of the cultures, while higher concentrations were detrimental. Rooting of the microshoots was most efficiently induced on MS medium supplemented with 2.5 lM indole-3-butyric acid (IBA) where a maximum of 3.3 roots per shoot with an average root length of 3.2 cm were recorded. Exposure of cultures to optimized cobalt concentration enhanced the rhizogenic competence of the microshoots resulting in a greater percentage (83.5 %) of rooting on the same medium as compared to unexposed cultures (74 %). Genetic stability of the clones exposed to optimum cobalt concentration was established by screening of 570 bands produced by 10 ISSR-PCR primers.