We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China. The genetic structure analysis showed that these rice varieties were distinctly divided into two populations, indica and japonica. The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components. The differences in indica/japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These results will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China. We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been cultivated from the 1950s to the 1990s in China. The genetic structure analysis showed The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica / japonica components. The differences in indica / japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These re sults will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.