Enshi, located in Middle China, is a typical seleniferous area of the world. Rice is the most important Selenium(Se) exposure source to local residents in Enshi, however, the translocation of Se in the soil-rice system remains poorly understood. The present study assessed the major Se fractions in Se-rich soils and which soil Se fractions are bioavailable for rice plants grown in Enshi. Rice plants and corresponding rhizosphere soils were collected throughout Enshi. Different soil Se fractions were extracted using sequential chemical extraction method. Soil organic matter (SOM) and soil pH were measured to understand their influences on Se transformation in soils. The concentration and bioaccumulation factors were investigated to understand the translocation of Se from soil to rice. The results showed that soil Se fractions are largely controlled by soil organic matter (SOM) contents. Decomposition of organic matter results in low SOM levels, which promote the transformation of organic-bound Se to water-soluble Se and ligand-exchangeable Se. Water-soluble, ligand-exchangeable and organic-bound Se fractions are the major sources of Se in rice tissues in Enshi. The structural equation modeling(SEM) applied in this study also support our conclusions well. This study will provide insights on biogeochemistry of Se in seleniferous area.