Nineteen polymorphic bands generated from 7 primers were established through RAPD, SSR, and ISSR-PCR analysis of the R2 generation of spontaneous diploidized pepper regenerants. Theoretically, all polymorphic PCR bands were derived from locus-specific sequence rearrangements in the genome, and they resulted from meiotic recombination during male gametogenesis. This created new binding sites in the genome of RAPD primers or SSR/ISSR, thus forming new PCR bands (Gyulai et al., 1999, 2000). The direct selection of DH progeny by molecular markers can be facilitated with RAPD