In order to analyze the genetic basis and indica-japonica differentiation of 35 weedy rice and 36 japonica rice in northeast of China, 88 pairs of molecular markers were used. The results indicated that the 88 selected markers can be applied extensively for the indica-japonica classification of rice, and total of 156 alleles identified by 88 markers with the average Na value was 1.773. Genetic diversity analysis revealed a little higher diversity level of weedy rice to the cultivars in northern China, with the average Na, He, Hsk and PIC value of 1.659, 0.006, 0.076, 0.085 for weedy rice, to 1.557, 0.004, 0.060, 0.067 for the cultivars, respectively. Genetic structure and NJ cluster analysis indicated that both weedy rice and cultivars had indica-japonica differentiation, which implied they had near relationships. Furthermore, the indica genotype frequency (Fi) of weedy rice was 0.050 which is higher than cultivars of 0.043. The trends for the Fi levels of weedy rice and cultivars in northeast of China were: weedy rice from Liaoning province (0.062)＞cultivars from Liaoning province (0.058)＞cultivars from Jilin province (0.048)＞weedy rice from Heilongjiang province (0.041)＞weedy rice from Jilin province (0.024)＞cultivars from Heilongjiang province (0.020).