In situ hybridization, a powerful tool for the molecular cytogeneticist, can be used to physically map repetitive, low-copy, and unique DNA sequences in plant chromosomes. With the availability of a recombination map in Oryza sativa L. and an improved in situ hybridization technique, this study was designed to establish the relationship between the genetic and physical distances of the rice restriction fragment length polymorphism map. Analysis indicated that considerable variation can exist between genetic and physical maps. A 183-centimorgan linkage map for chromosome 2 covered less than 50% of the chromosome and did not include the centromere, whereas a 91-centimorgan linkage map for chromosome 1 covered approximately 80% of the chromosome. The results indicated that there are potential "hot" and "cold" spots of recombination and polymorphisms in rice, which involve both genes and restriction fragment length polymorphisms.