A new method for cloning genes that are known only by their phenotype, not their biochemical effect, has recently been developed. This strategy, which is known as map-based cloning, relies on knowledge of genetic map position as the basis for cloning genes of interest. In plant pathology, this includes many disease resistance genes in plants, as well as genes controlling race-specific avirulence in fungal plant pathogens. In this review, the major steps in map-based cloning are examined, namely, tagging genes of interest with tightly linked restriction fragment length polymorphic (RFLP) markers, physical mapping with pulsed-field gel electrophoresis, and chromosome walking with yeast artificial chromosomes. Criteria for deciding whether to adopt a map-based cloning strategy are also discussed.