The main carotenoid in the extremely radiation-resistant bacterium Deinococcus radiodurans is deinoxanthin. In this paper, based on UV-Vis, MS/MS spectra as well as the chemical properties, the other main two carotenoids in this bacterium were identified as ((all-E)-1-hydroxy-3,4-didehydro-1,2-dihydro-β,ψ-carotene-4-one-1), and ((all-E)-1-hydroxy-3,4-didehydro-1,2,2,3-quahydro-β,ψ-carotene-4-one-1), respectively. The fully structure elucidation for the carotenoids should help to gain a better understanding of the radiation-resistant mechanisms in this remarkable bacterium.