Iran is one of the centers of genetic diversity for cultivated and wild safflower species. Some of the wild species such as Carthamus oxyacantha having distribution and adaptability with different climate conditions could be used in safflower breeding programs. In this study, populations of wild safflower, C. oxyacantha were collected from western, central and southern regions of Iran to investigate their genetic variation for quantity and quality of seed oil, agro-morphologic traits and ISSR markers. The effect of seed coat color on resistance to safflower fly, Acanthiophilus helianthi was also evaluated. Furthermore, the inheritance and possibility of transferring seed coat color and other useful genes from wild species to cultivated one via interspecific hybridization was studied. The mechanism of plant resistance to safflower fly and effective bio-chemical compounds involved in the resistance were also investigated. Light and electron microscope were used to observe the color ingredients accumulation part in the seed coat. Finally, the effect of seed color on seed yield and other agronomic traits of safflower and fly resistance were studied in F 3 generation derived from the interspecific hybridization. Evaluation of genetic diversity among wild safflower accessions using morphologic traits and ISSR markers showed that there were considerable variation among the wild accession and based on clustering, they were separated according to their different geographical regions. The results showed that some wild accessions had appropriate seed oil content and oil quality comparable with the oil extracted from cultivated species. In the wild safflower germplasm, colored seeds (brown and black) had higher frequency; higher seed weight and lower percentage of safflower fly damage compared to the white seeds. Higher dead fly larvae in the heads and lower infected heads resulted in lower fly density and seed yield damage in the wild safflower accessions than the cultivated species. This may indicate that wild species are possibly resistant to safflower fly. Detection of different polyphenolic- flavonoid compounds in colored seed coats showed that these compounds may involve in antibiosis of fly larvae. Study of F 2 and F 3 progenies of interspecific cross showed that two loci with epistatic action may control seed coat color. Also, evaluation and comparison of F 3 population having white or colored seed coats in the field showed that plants derived from colored seed had better seedling characteristics and earliness, higher yield and yield components specially the number of heads per plant, but lower seed hull percentage. Seed coat color had also significant effect on safflower fly damage. The number of eggs and