Apomixis, asexual reproduction through seed, is an obligate mode of reproduction in several species from the genus Pennisetum. Transfer of apomixis to sexual, cultivated pearl millet (P. glaucum) from a wild species P. squamulatum has resulted in an obligate apomictic backcross line with a low, but unknown number, of chromosomes from the wild species. Molecular markers (restriction fragment length polymorphisms and random amplified polymorphic DNAs) have been identified that unequivocally demonstrate the presence of P. squamulatum DNA in BC3. Three of the informative RFLP clones have been sequenced and converted to sequence-tagged sites that can be amplified by the polymerase chain reaction. Molecular genetic analysis of more advanced back-cross individuals, using the two types of polymerase chain reaction-based molecular markers, has demonstrated co-inheritance of apomictic reproduction and two of the molecular markers. The remaining five molecular markers generally co-segregate with each other but are not linked with the mode of reproduction. These results suggest that genes for apomixis apparently can be transmitted by a single chromosome. Chromosome-specific markers will provide a starting point for the mapping of this genetically intractable reproductive trait.