Abstract: AimTo investigate the intraspecific variation of Carthamus tinctorius L. (safflower) and establish foundation for further breeding of safflower germplasm resource and screening the quality correlation genes. MethodsAmplified fragment length polymorphism (AFLP) was carried out to analyze genetic variation of 28 safflower populations collected in China. Unweighed pair-group method of with arithmetical averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among the populations. ResultsAll populations could be uniquely distinguished using 12 selected primer combinations. Similarity coefficients ranged from 0.48 to 0.96 among the populations. Dendrogram revealed distinct segregation of all the cultivars into three main groups and one midst group. ConclusionLimited genetic diversity exists within the tested 28 collections at intra specific level and AFLP-based phylogeny was not absolutely consistent with that based on morphological characters may be due to the interaction effect between genotype and environment.