Genetic linkage mapping and QTL analysis of important phenotypic traits are currently active areas of research regarding agronomically important plants and animals. Marker assisted breeding based on linkage maps and QTLs is likely to be one of the most important and broadly useful applications of biotechnology in agriculture. Current genetic linkage mapping uses almost exclusively molecular markers and is based on DNA sequence polymorphisms between parents whose segregation is followed in their progeny. To improve the efficiency of marker generation, we have developed a simple, and reasonable-cost method of polymorphism detection termed dideoxy polymorphism scanning. The method was developed using denaturing acrylamide sequencing gels. It has also been adapted to high-throughput capillary sequencing machines. This method is simple and efficient in identification of gene-based polymorphisms that can be used for genetic linkage mapping. Since most of the time required to develop a gene-based linkage map is spent in identification of useful polymorphisms, this method will significantly shorten the time required for map generation.