The effects of basal-applied selenate, selenite and selenomethionine (SeMet) (0 – 0.8 mg/kg) on selenium accumulation in Flammulina velutipes were studied in soil-less culture. Results showed that Se contents in Flammulina velutipes fruiting body and base increased significantly with the increase of Se addition. The application of selenite showed better effect than SeMet and selenate in increasing Se content in Flammulina velutipes. For the substrate amended with 0.8 mg/kg selenite, selenate and SeMet, the Se levels in fruiting body were 0.24, 0.12 and 0.08 mg/kg (fresh mass), respectively. The recovery (fruiting body and root) of Se applied as selenite was greater than SeMet and selenate. What’s more, the recovery of Se in fruiting body in SeMet and selenate decreased significantly from 14.28% to 6.33% and from 13.67% to 3.70%, respectively, with the increase of Se levels in substrate; while no significant difference in the recovery (fruiting body) of Se among different Se levels when applied selenite.