The phenotypically uniform indica rice variety IR64 was chosen for study of the source and inheritance of within cultivar residual variation using a set of SSR markers.Molecular heterogeneity in IR64 was identified on the short arm of chromosome 2 involving at least five SSR loci spanning nearly 30 cM.The SSR variations originated from the parental lines of IR64(IR5657-33-2 /IR2061-465-1-5-5)and were segregating in the selfed bulk seed stock in a Mendelian manner for more than 20 years.This study was one of few examples to verify successfully that within cultivar variations of SSR in morphologically uniform selfing crops came from its parental lines,which has immediate and commercial applications including test of seed purity,varietal fingerprinting,and curation and propagation of germplasm collections. The phenotypically uniform indica rice variety IR64 was chosen for study of the source and inheritance of within cultivar residual variation using a set of SSR markers. Molecular heterogeneity in IR64 was identified on the short arm of chromosome 2 involving at least five SSR loci spanning nearly 30 cM.The SSR variations originated from the parental lines of IR64 (IR5657-33-2 / IR2061-465-1-5-5) and were segregating in the selfed bulk seed stock in a Mendelian manner for more than 20 years.This study was one of few examples to verify successfully that within cultivar variations of SSR in morphologically uniform selfing crops came from its parental lines, which has immediate and commercial applications including test of seed purity, varietal fingerprinting, and curation and propagation of germplasm collections.