Herbaspirillum sp. WT00C is a tea-plant-specific endophytic bacterium. A genomic survey revealed an intact pathway for selenocompound metabolism in the genome of this bacterium. When it was cultured with sodium selenate, Herbaspirillum sp. WT00C was able to turn the culture medium to red. Electron microscopy and energy-dispersive X-ray spectroscopy confirmed that Herbaspirillum sp. WT00C reduced selenite (Se6+) to elemental selenium (Se0), and selenium nanoparticles (SeNPs) were secreted outside bacterial cells and grew increasingly larger to form Se-nanospheres and finally crystallized to form selenoflowers. Biochemical assays showed that selenospheres contained proteins but not carbohydrates or lipids. The improvement of selenium enrichment of tea plants by Herbaspirillum sp. WT00C was also tested. After Herbaspirillum sp. WT00C was inoculated into tea seedlings via needle injection and soaking tea-cutting methods, this endophytic bacterium markedly enhanced selenium enrichment of tea. When the tea seedlings inoculated by soaking tea-cutting mode were cultivated in the selenium-containing soils, selenium contents of tea leaves in three experimental groups were more than twofold compared to those of control groups. Our study demonstrates that the endophytic bacterium Herbaspirillum sp. WT00C has the ability to reduce selenate and improve selenium enrichment of tea.