Selenium (Se) is a dietary essential trace element for humans with various physiological functions and it could also be accumulated by some plant species, like Astragalus bisulcatus, Stanleya pinnata, and Cardamine hupinshanensis. A novel Gram‐stain‐negative, facultatively anaerobic, selenite‐tolerant bacterium, designated strain YLX‐1T, was isolated from the rhizosphere of a Se hyperaccumulating plant, Cardamine hupingshanensis in Enshi, China. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that strain YLX‐1T is a potential new species in the genus Wautersiella. Strain YLX‐1T could grow in the temperature range of 4–37°C (optimally at 28°C) and in the pH range of 5–9 (optimum pH 7), which also could tolerate Se up to 6000 mg Se/L via producing extracellular red nano‐Se with 100–300 nm size. However, it could predominantly accumulate selenocystine (SeCys2) in the cell under lower Se stress (1.5 mg Se/L). These results would help broaden our knowledge about the Se accumulation and transformation mechanism involved in rhizosphere bacteria like strain YLX‐1T in C. hupingshanensis. Based on polyphasic data, we propose the creation of the new species Wautersiella enshiensis sp. nov., strain YLX‐1T ( = CCTCC M 2013671) which will be promising to produce nano‐Se as fertilizer, food additives or medicine.