Ranunculus wallichianus is a medicinally important plant and an endemic species to Western Ghats of South India. An e cient and reliable indirect regeneration protocol system for R. wallichianus was developed from leaf explants in the present investigation. Leaf explants were cultured on both fullstrength and half-strength MS (Murashige & Skoog) medium supplemented with different concentrations (1.0 mg L − 1 to 3.0 mg L − 1 ) of 2,4-D and NAA. Among the different concentrations tested, the highest percentage of yellowish green compact nodular callus formation was observed on half-strength MS medium with 2.0 mg L − 1 of 2, 4-D. Then, the in vitro raised organogenic callus was cultured on half strength MS medium containing various concentrations (1.0 mg L − 1 to 3.0 mg L − 1 ) of BA, KIN and TDZ with 0.5 mg L − 1 NAA and 10% CW for in vitro shoot regeneration. The highest percentage of regeneration response (97%) and maximum number of shoots formation (11.1 ± 0.13 shoots/culture with 9.2 ± 0.35 cm mean shoot length) were obtained from MS medium containing 2.5 mg L − 1 BA with 0.5 mg L − 1 NAA and 10% CW. The well elongated in vitro raised shoots were rooted in half strength MS medium with 2.5 mg L − 1 IBA + 250 mg L − 1 activated charcoal shows high frequency of root formation. The well rooted plantlets were successfully hardened and acclimatized with the survival rate of 94%. Clonal delity of in vitro raised plantlets was assessed by using DNA based RAPD and ISSR molecular markers. The total of 56 and 47 monomorphic bands were obtained from RAPD and ISSR markers respectively. This present in vitro propagation protocol system could be an effective for the conservation of R. wallichianus with their genetic purity and its further investigations.