Association of ISSR markers with some biochemical traits of Valeriana jatamansi Jones

► Association of ISSR markers with phytochemicals and antioxidant activity in Valeriana jatamansi were established. ► Among 97 ISSR markers, only three ISSR markers exhibited significant (p < 0.05) association with antioxidant activity. ► The method can be useful for selection of the genotypes/populations with high antioxidant activity. ► The result has commercial applications as suitable genotypes of the species are needed by pharmaceutical industries.