The use of appropriate selection methods are important to increase yield in breeding programs. Utilization of selection indices is one of the most effective method for selection of superior genotypes to improve the complex traits such as seed yield. In order to evaluate the efficiency of different selection methods, families of two F populations derived from interspecific hybridization of Carthamus tinctorius × Carthamus oxyacanthus (IO) and Carthamus palaestinus × Carthamus tinctorius (IP) were evaluated under two moisture environments (normal and drought-stress) at the research farm of Isfahan University of Technology during. The Smith-Hazel , Smith-Hazel and Pesek-Baker indices were measured based on the traits entered in step-wise regression model. The results indicated that under normal conditions, Pesek-Baker index was more effective than the Smith-Hazel and Smith-Hazel and was also more efficient for the selection of superior genotypes in IP population. Also, the Smith-Hazel and Smith-Hazel indices were more effective than Pesek-Baker index under drought-stress conditions in this population. Smith-Hazel and Smith-Hazel indices were more effective than Pesek-Baker index in IO population at two moisture environments. Efficiency of selection in IP population was more than IO population, thereby it can be used to develop superior genotypes in breeding programs. Since the C. palaestinus have less undesirable characters compared to other wild parents, it may be suitable source for transferring desirable genes to the cultivated species.