Pruatjan (Pimpinella pruatjan Molk.) is an Indonesian endangered medicinal plant, so that it is highly protected. Cryopreservation can be applied to this plant for long-term preservation. The aim of this research was to obtain a method of encapsulation-vitrification by optimizing each step in cryopreservation protocol i.e. preculture, loading, dehydration with and without freezing in liquid nitrogen. The best treatment of each step would be applied in the following step. On preculture experiment, in vitro shoots were planted on the Driver and Kuniyaki (DKW) basal media containing 0.3 M sucrose and incubated for 1, 2, 3, 4, and 5 days. After those incubation period, shoot tips were encapsulated with 2.5% Na-alginate and soaking for 15 minutes in 100 ppm CaCl2 solution before planting. On loading experiment, precultured explants were loaded in DKW basal solution containing 2 M glycerol and 0.4 M sucrose for 0, 30, 60, and 90 minutes. On dehydration experiment, preculturead and loaded explants were dehydrated with PVS2 solution PVS2 (DKW + 30% glycerol + 15% DMSO + 15% ethyleneglicol + 0.4 M sucrose) for 0, 30, 60, 90, and 120 minutes. The parts of them were freezed in liquid nitrogen (-196oC). The result showed that cryopreservation through encapsulation-vitrification technique could be applied on pruatjan. The best preculture treatment was 5 days incubation period. The best loading treatment was 30 minutes. The best dehydration treatment was 90 minutes. The successful level of this research was still low (10%) so that it needs optimization method.