This study analyzed the genetic diversity and indica-japonica gene frequencies of Jiangyong wild rice (Oryza rufipogon Griff.) populations, which were sampled in 1982, 2008 and 2017, using 39 SSR markers and 38 Indel markers respectively. The results showed that the genetic diversity of 40 accessions sampled and conserved in ex-situ in 1982 was higher than that in-situ conservation sampled in 2008 and 2017. No significant difference was observed in genetic diversity between the samples in 2008 and 2017. In addition, samples collected in different years displayed unobvious differentiation, with low genetic differentiation coefficient(Fst) and high gene flow(Nm). According to cluster analysis and principal coordinate analysis, we found that the genetic relationship between wild rice and japonica rice is closer than that between wild rice and indica rice. Most of the wild rice plants were grouped to japonica class, and a few belong to japonicaclinous class. In 2008, the percentage of japonicaclinous individuals increased by 10.0% compared with 1982, and in 2017, the percentage increased by 1.6% compared with 2008. These results implied that the indica gene frequency of wild rice increased with the environmental changes of in-situ conservation.