Abstract Bioavailability and ecological effects of selenium (Se) in soil depend on its species. Samples of 15 kinds of soils were collected in China for analysis of Se species using a sequential extraction method proposed by Qu in 1997. Se in soil may be partitioned into: 1) soluble Se (SOL-Se), 2) exchangeable Se and Se bound to carbonate(EX-Se), 3) Se bound to Fe–Mn oxides(FMO-Se), 4) Se bound to organic matters(OM-Se), 5) residual Se(RES-Se). Relationship between soil physico-chemical properties and Se species were determined with path analysis on Amos 18.0. Results show that OM-Se dominated in all the soils, except for black soil from Heilongjiang and red soil (in paddy field and upland) from Jiangxi where RES-Se did. SOL-Se accounted for only 0.4%~14.6% of the total Se. EX-Se and OM-Se were in significant positive correlation with RES-Se. However, no significant correlations of SOL-Se and FMO-Se with other Se species were observed. Path analysis indicates that organic matter negatively affected FMO-Se, while positively affected all other species. Amorphous iron showed no effect on SOL-Se, but it did stronger effect on the other four Se species than organic matter did. Except for SQL-Se, organic matter and amorphous iron had the strongest impact on OM-Se and RES-Se, respectively. pH and clay influenced Se speciation via their negative or positive effect on organic matter and amorphous iron, respectively. To conclude, organic matter and amorphous iron are two decisive factors affecting Se partition in soil. Nevertheless, the effects of pH and clay are far from negligible.