This study aimed to identify the optimal treatment conditions for ethyl methanesulfonate(EMS)mutagenesis of Isodon lophanthoides var.graciliflorus seeds and analyze the phenotypic variations of selected mutant plants using ISSR and SSR molecular markers.A mutant library of I.lophanthoides var.graciliflo-rus was constructed to provide materials for the study of germplasm innovation and utilization in I.lophan-thoides var.graciliflorus.1.2%EMS treatment for 7 hours is the optimal mutagenic treatment for the seeds of I.lophanthoides var.graciliflorus.Using EMS mutagenesis treatment,3 000 seeds of I.lophanthoides var.graciliflorus were treated.Phenotypic identification was performed on 1 262 mature M1 generation plants obtained.A total of 489 phenotypic variation plants were selected,with a mutation frequency of 38.7%.The phenotypic variations included high straw,dwarf,thick stem,thin stem,branching,multi-branching,and dark leaf color.From the M2 generation,four individual plants with excellent traits were preliminarily selected based on phenotypic identification.The results of ISSR analysis showed that 9 primers amplified a total of 72 loci,with an average of 8 loci per primer.Among them,54 loci were polymorphic,accounting for a polymor-phism rate of 75.00%.The genetic similarity coefficient between the 22 phenotypic variant plants and the con-trol group ranged from 0.638 9 to 0.847 2.The results of SSR analysis showed that 13 pairs of SSR primers amplified a total of 86 loci,with an average of 7.81 loci per primer.Among them,54 loci were polymorphic,accounting for a polymorphism rate of 62.79%.The genetic similarity coefficient between the 22 phenotypic variant plants and the control group ranged from 0.590 5 to 0.828 6.Both the clustering analysis based on ISSR and SSR results indicated that the control group could be distinguished from the majority of the pheno-typic variant plants,suggesting that most of the induced mutant plants had certain genetic differences from the control group at the molecular level.