The rules of the genetic code are established by aminoacylations of transfer RNAs by aminoacyl tRNA synthetases. New codon assignments, and the introduction of new kinds of amino acids, are blocked by vigorous tRNA-dependent editing reactions occurring at hydrolytic sites embedded within specialized domains in the synthetases. For some synthetases, these domains were present at the time of the last common ancestor and were fixed in evolution through all three of the kingdoms of life. Significantly, a well characterized domain for editing found in bacterial and eukaryotic threonyl- and all alanyl-tRNA synthetases is missing from archaebacterial threonine enzymes. Here we show that the archaebacterial Methanosarcina mazei ThrRS efficiently misactivates serine, but does not fuse serine to tRNA. Consistent with this observation, the enzyme cleared serine that was linked to threonine-specific tRNAs. M. mazei and most other archaebacterial ThrRSs have a domain, N2(A), fused to the N terminus and not found in bacterial or eukaryotic orthologs. Mutations at conserved residues in this domain led to an inability to clear threonine-specific tRNA mischarged with serine. Thus, these results demonstrate a domain for editing that is distinct from all others, is restricted to just one branch of the tree of life, and was most likely added to archaebacterial ThrRSs after the eukaryote/archaebacteria split.