Differential regeneration potentiality of two cotyledons (Cot and Cot E) of Vigna radiata seed during in vitro shoot differentiation is now well established. In the present study, endogenous abscisic acid (ABA) level (both bound and free form) was estimated using high performance liquid chromatography technique from these two explant types prior to the induction of in vitro differentiation. Both free and conjugated forms of endogenous ABA were higher in Cot than Cot E. However, the bound form of ABA was higher than free or active form in both the explants. Effects of an ABA catabolic inhibitor, diniconazole on the endogenous ABA production potential were determined. Diniconazole inhibits ABA 8’-hydroxylase, the catabolizing enzyme, resulting in accumulation of free ABA in the cell. It was noted that diniconazole inhibited bound form of ABA formation in a concentration dependant manner with a concomitant increase in the free form and decrease in shoot differentiation from Cot E explants. Likewise, exogenously applied ABA in in vitro culture also resulted in decrease in shoot regeneration frequency from the cotyledonary explants ascertaining the differential level of endogenous ABA is one of the determinants of differential regeneration response of Cot and Cot E under in vitro cultural condition. Cytokinin antagonized inhibitory effect of ABA mediated by cytokinin responsive proteins, such proteins are up regulated differentially in Cot E has recently shown us through proteomic study confirming further the role of ABA.