Aconitum carmichaeli Debx. is an important medicinal herb in China, it has abundance germplasm and relatives in the same genus. In this study, we employed SSR markers to analyses 51 individuals of A. carmichaeli. sampled from 17 populations and its 65 relatives from 13 species in genus Aconitum L.. Genetic diversity, genetic differentiation and phylogenetic relationship of the individuals and species were revealed. As the results, （1）11 SSR primer pairs used in this study are stable and polymorphic, 109 alleles were screened out totally, with the average of 9.91 per pair. （2） The genetic diversity of A. carmichaeli is abundance (A=3.090 9，I=0.889 7，h=0.540 2), the genetic differentiation among populations is obvious (G_st=0.277 4). High polymorphism (A=9.909 1, I=1.526 2, h=0.690 5), pronounced genetic differentiation (F_st=0.437) and limited gene flow among species (N_m=0.451 8) were detected in the 14 species in genus Aconitum. （3） Cluster analysis revealed that most of the A. carmichaeli individuals sampled from the same population clustered together formed 17 small clades, and then formed a clade; as for those relatives, samples of same species clustered together and form different clades individually; 14 species of genus Aconitum formed 5 big clades, which is consistent with the result of traditional taxonomy. （4）6 primer pairs (Tchin03, Tchin04 Tchin20, Tchin26, Tchin29 and Tchin32), which performed higher polymorphic and more abundance genotype were chosen to construct the fingerprinting for A. carmichaeli germplasms and its relatives. The study provides reliable molecular basis for classification and identification for A. carmichaeli germplasm and its relatives in the same genus.