Carthamus (Asteraceae) contains both crop species (C. tinctorius, safflower) and weedy species, increasing the need for a better understanding of the genus. Despite previous studies, many outstanding questions remain regarding the phylogenetic relationships of safflower, especially with regards to the weedy species. Investigation of the relationships in Carthamus was done using sequence data. The closest relative to C. tinctorius was studied using microsatellite data. Microsatellite data was also utilized to track the introgression of C. oxyacanthus DNA into the C. tinctorius genome in an interspecific cross. Sequence data supports the division of the genus into two sections, Carthamus and Atractylis. Both sequence and microsatellite data reveal that most traditionally recognized species are not monophyletic. Microsatellite data indicates that C. palaestinus is the closest relative of cultivated safflower. Microsatellites also indicate that C. oxyacanthus DNA is able to move into the C. tinctorius genome, showing potential for breeding programs and raising concerns for potential transgenic crops.