The genus Berberis have high significance in Indian and other traditional systems of medicine due to the presence of iso-quinoline alkaloids. The present study was conducted to record the metabolic variation in eight Berberis spp. collected from the Western Himalayan region. The RP-HPLC-PDA chromatogram separates the markers jatrorrhizine, palmatine and berberine at specific retention time, 11.45, 16.41 and 18.15 minutes respectively. The method was validated on linearity, precision and recovery indices as per ICH (International Conference on Harmonisation) guidelines. The maximum content of berberine, palmatine, and jatrorrhizine was found in Berberis asiatica (1.74% ± 0.032, 1.63% ± 0.028 and 0.264% ± 0.012 respectively) on % dry weight basis. This study will help in phyto-marker based identification and differentiation 2 of various Berberis species, which can be used as an alternative to the official drug Daruharidra i.e., Berberis aristata.