Seventeen morphological marker genes were associated with restriction fragment length polymorphism markers in rice by using four F-2 populations, each segregating for a few observable traits, and 14 near isogenic lines (NILs), each containing one morphological mutant gene. The location of five genes was confirmed on the basis of F-2 analysis: Purple bull (Pr) (16.8 +/- 7.9 cM away from RG163 on chromosome 4); Phenol staining (Ph) (20.8 +/- 8.4 cM away from RG163 on chromosome 4); glabrous leaf and hull (gl-l) (14.3 +/- 7.4 cM away from RG182, and 20.9 +/- 8.3 cM from RG403 on chromosome 5); Brown pericarp (Re) (12.5 +/- 7.2 cM away from RG30 on chromosome 7); and lazy growth habit (la) (28.8 +/- 9.4 ci?A away from RG118 on chromosome 11). In addition, 12 other morphological markers, including the agronomically important genes semidwarf (sd-l) and Pollen restoring factor (Rf-l) were tentatively associated with mapped DNA clones based on screening pairs of NILs.