Cytosine bases can be deaminated spontaneously to uracil, causing DNA damage. Uracil‐DNA glycosylase (UDG), a ubiquitous uracil‐excising enzyme found in bacteria and eukaryotes, is one of the enzymes that repair this kind of DNA damage. To date, no UDG‐coding gene has been identified in Methanococcus jannaschii, although its entire genome was deciphered. Here, we have identified and characterized a novel UDG from M.jannaschii designated as MjUDG. It efficiently removed uracil from both single‐ and double‐stranded DNA. MjUDG also catalyzes the excision of 8‐oxoguanine from DNA. MjUDG has a helix–hairpin–helix motif and a [4Fe–4S]‐binding cluster that is considered to be important for the DNA binding and catalytic activity. Although MjUDG shares these features with other structural families such as endonuclease III and mismatch‐specific DNA glycosylase (MIG), unique conserved amino acids and substrate specificity distinguish MjUDG from other families. Also, a homologous member of MjUDG was identified in Aquifex aeolicus. We report that MjUDG belongs to a novel UDG family that has not been described to date.