Diversity and also the molecular analysis of genotypes and association analysis among molecular markers and quantitative traits are the important methods in breeding programs. In this study, 30 safflower genotypes were evaluated in the research farm of the Graduate University of Advanced Technology, Kerman, Iran based on randomized complete block design with three replications. The phenotypic and agronomic traits were evaluated and, also, these genotypes were studied with 24 start codon targeted polymorphism (SCoT) and 10 inter-simple sequence repeat (ISSR) markers at the molecular level. The differences among genotypes were significant for the studied traits based on analysis of variance. The genotypes divided into three groups by using cluster analysis based on quantitative traits. Cluster analysis method by Jaccard's similarity coefficient as well as Bayesian statistical method based on molecular data classified genotypes into two groups. The molecular variance analysis showed that diversity among populations is much more than within populations. Nineteen and thirty one gene loci had identified by (G + P + K) and (G + P + K + Q) of mixed linear model for the studied traits, and some of these loci were the same in two models. Some of these markers controlled several traits that named co-location markers, so these markers are effective in plant breeding programs. The SCoT and ISSR markers can be developed as the sequence-tagged site markers and used in marker-assisted selection and breeding programs of safflower genotypes when they linked to agronomic traits.