A number of recombination-based and physical mapping methods have been developed in order to study and understand the genomic organization of plant species. Of these methods, physical mapping methods provide the best correlation between position on a map and actual physical location on the chromosome. In this review, we discuss differences between maps developed on the basis of recombination and those developed independent of recombination. In the latter method, termed commonly as physical mapping, we discuss methods that have been employed in a number of agriculturally important plant species including rice, the legume model Medicago, tomato, soybean, barley and wheat, and then focus on the radiation hybrid method of physical mapping. After a brief overview of the radiation hybrid methods employed in mammalian species, we discuss radiation hybrid mapping for maize, barley, cotton and wheat in detail.