RESEARCH S afflower (Carthamus tinctorius L.) is an ancient crop with numerous past and present uses (Li and Mündel, 1996). Traditionally saffl ower was grown for its fl owers, which were used as a fabric dye, and for food coloring, fl avoring, and medicinal purposes. Today, seeds are the major plant part used, resulting in a high quality edible and industrial oil and bird feed (Knowles, 1989). Newer uses include production of transgenic pharmaceuticals (McPherson et al., 2004), biofuel, and specialty oil types to improve human diet (Velasco and Fernández-Martínez, 2004). Saffl ower, a diploid with 12 chromosome pairs (Ashri and Knowles, 1960), is a predominately self-pollinating species, but has the potential for considerable outcrossing with pollen transfer by a variety of insects (Butler et al., 1966). The USDA-ARS maintains a collection of saffl ower germplasm at the Western Regional Plant Introduction Station (WRPIS), Pullman, WA, which currently includes more than 2300 accessions. These accessions, representing germplasm from more than 50 countries, are available without charge to scientists worldwide. Molecular markers can be used for identifying duplicate accessions, developing and testing special groups within collections (such as core collections), estimating and comparing diversity