Addition of encapsulated anthocyanins in margarine formulation improved the stability of margarine. In this study, investigation on the storage and stability characteristics of water-in-oil emulsion, i.e. margarine, containing encapsulated or non-encapsulated anthocyanins from roselle and red cabbage was carried out. Encapsulation of anthocyanins was performed using microwave-assisted technique to study the dispersion and stability of anthocyanins in the margarine. Margarines were formulated with three different oil-to-aqueous ratios (75:25, 80:20 and 85:15). The stability of the margarine was determined by using Solid Fat Content, thermal and phase stability analysis. Margarine containing encapsulated anthocyanin showed improved stability compared to non-encapsulated anthocyanin.