The use of positional approaches for the isolation of genes from most crop species is difficult due to the large size of their genomes. If the order of genes in segments of the genomes is similar in different plants, it might be feasible to use smaller genomes as templates upon which to base strategies for the positional cloning of genes from other species. Comparative genetic mapping, using markers such as restriction-fragment length polymorphisms, has revealed extensive conservation of long-range genome organization (macrostructure) between related species. But is the organization of the tens or hundreds of genes between the genetic markers also conserved? Recent results suggest that the fine-scale structure (microstructure) of plant genomes is more dynamic than previously assumed from investigations of the macrostructure.