Selenium is an essential trace element for many living organisms. However, it is still not clear about the biogeochemical cycle of selenium in high soil selenium content area. In this study, an extremely high selenium tolerant bacteria, Lelliottia amnigena YTB01 were isolated in Enshi, China, with the minimum IC100 of Na₂SeO₃ 35 g/L, more than previous studies have reported. The Lelliottia amnigena YTB01 strain genome was sequenced using a PacBio RS II platform and Illumina HiSeq 4000 platform (BGI, Shenzhen, China). The genome sequencing identified that Lelliottia amnigena YTB01 is 4,941,692 bp and has a G+C content of 54.43%, including 4,605 coding genes and 141 ncRNA. Comparison to the genome of Lelliottia amnigena ZB04, selenocysteine translation elongation factor is specific in YTB01, which play an important role in regulating selenocysteine biosynthesis. Furtherly, the KEGG database annotation revealed important metabolic pathways about selenocysteine synthesis, methyltransferases, DNA repair (detoxification related), and also showed metabolism of selenium is coupled with that of nitrogen and sulfur in Lelliottia amnigena YTB01. Our finding revealed the key mechanisms of selenium metabolism and detoxification in high selenium tolerant bacteria.