Mapping and application of restriction fragment length polymorphisms (RFLPs) in polyploids has lagged behind diploids due to complications from (i) a large number of segregating genotypes, (ii) comigration of fragments, (iii) poorly characterized genome constitution nod/or chromosome pairing behavior, and (iv) complicated genotype characterization due to multiple fragments. Strategies that facilitate mapping in polyploids include linkage maps for diploid relatives, aneuploid stocks, and haploid or doubled haploid populations; however, each approach has advantages and disadvantages for different species. This review relates primarily to those polyploids with regular bivalent pairing, since multivalent pairing can result in double reduction and aneuploidy, further complicating linkage analysis. The use of single‐dose restriction fragments for segregation and linkage analyses can greatly reduce the complexity of mapping in polyploids. Because of the large difference between disomic and polysomic polyploids in detection of repulsion phase linkage, a comparison of the number of coupling‐ and repulsion‐phase linkages will provide an indication of the degree of preferential pairing among chromosomes in each linkage group. When diploid relatives are used for mapping, probe library survey filters must contain a lane for each species being mapped, clones must be polymorphic for parents of each species mapping population, new fragments with a different molecular weight may map to different locations in the polyploid because of structural rearrangements, genomes must be relatively homosequential or rearrangements well characterized, and the diploid population should exhibit a high level of polymorphism. Aneuploid or deficiency genetic stocks can be efficiently employed for mapping fragments for species exhibiting moderate to low polymorphism, because nearly every fragment hybridizing to a probe is assigned to a chromosome or subchromosomal location. This approach does not depend on regular meiosis in a hybrid, thus avoiding the problem of chromosomal rearrangements, abnormal pairing, and sterility in wide crosses. Where aneuploids are not available, markers can be used to advantage in developing such genetic stocks. Inbred populations have significant advantages for mapping because of the reproducibility of the genotypes and the absence of heterozygotes. Exotic genotypes and alien germplasm are prime sources of novel alleles for economically important traits. In the future, the breeder will be able to cross different genotypes that are known to possess positive alleles at different loci and, using markers for those alleles, select transgressive segregates. With this technology, breeders will likely incorporate many novel alleles for agronomic traits from alien species into elite cultivars.