To illuminate the migration and transformation of selenium (Se) in the igneous rock-soil-rice system, 285 pairs of rhizosphere soil and rice samples were collected from the granitoid and basalt areas in Hainan Province, South China. The contents of Se in soils derived from granitoid and basalt are, respectively, 0.19±0.12 mg/kg and 0.34±0.39 mg/kg, which are much higher than Se contents in granitoid and basalt. Selenium shows remarkable enrichment from granitoid and basalt to soils. The mobile fraction of Se in soils derived from granitoid is 0.0100±0.0034 mg/kg, which is significantly higher than that of basalt (0.0058±0.0039 mg/kg). Although soil derived from basalt shows higher Se contents, Se contents in rice samples, mobile fractions of Se in soils, and biological concentration factor (BCF) is similar or even lower than that from granitoid. Basalt consist of calcic plagioclase and pyroxene, and are much richer in Fe, Al, and Ca than granitoid. Correspondingly, the basalt-derived soils have higher goethite, hematite, kaolinite, cation exchange capacity (CEC) content, and higher pH than the granitoid-derived soils, which result in higher adsorption capacity for Se and relatively lower Se bioavailability. Soils derived from granitoid and basalt in tropical regions are beneficial to produce Se-rich rice.