Polymerase chain reaction (PCR), with single ten-base-long nucleotide primers, was used to amplify random regions of genomic DNA from eleven diploid meiotic mutants (2n egg, 2n pollen and jumbo pollen producers) of the Medicago sativa-coerulea-falcata complex. Electrophoretic patterns of the resulting random amplified polymorphic DNA (RAPD) fragments were evaluated to develop a graphical representation of amplification products from which conserved and individual-specific markers could be readily identified. Oligonucleotide primers differed significantly in their capacity of detecting polymorphism. Jumbo pollen (jp) mutants showed higher levels of similarity, as proportion of shared amplification products, than 2n pollen mutants. A diploid plant of alfalfa, tested for the occurrence of two mechanisms of unreduced egg formation (second division restitution and apomeiosis) was analyzed to obtain genome specific fingerprints. This PCR-based characterization could be used to determine whether the apomeiotic 2n eggs develop through parthenogenesis. The application of RAPD markers for germplasm evaluation and alfalfa improvement programs is also discussed.