Proso millet occurs both as a crop and a weed in North America. In 1970, an olive-black seeded biotype called ‘wild proso millet’ was found as an aggressive weed in row crops in Minnesota and Wisconsin and has since spread over a large area. We used Random Amplified Polymorphic DNA (RAPD) to assess genetic relationships among biotypes, measure genetic variation within wild proso millet across its range, and detect hybridization between wild proso millet and crop biotypes of proso millet. We found 97 RAPD genotypes among 398 individuals: 69 wild proso millet genotypes, 26 crop and crop-like weed genotypes, and two hybrid genotypes. Five RAPD markers consistently differentiated wild proso millet from crop cultivars and crop-like weeds. About 10% of the genotypes had at least one marker of the other type, suggesting possible hybridization between wild proso millet and crop biotypes. Most genotypes occurred in only one or two of the over 100 populations tested. The most widespread wild proso millet genotype occurred in 12 populations distributed in North Dakota, Minnesota, Illinois, and Wisconsin. More genetic variation exists among populations of wild proso millet than expected for a plant that presumably experienced a severe genetic bottleneck only 20 generations ago. Hypermutation rates and crossing between wild proso millet and crop cultivars could not account for the degree of genetic variation found in wild proso millet. The pattern of genetic variation among wild proso millet populations suggests multiple introductions of wild proso millet to North America.