Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNASec) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNASec from the bacteriumAquifex aeolicus, in complex with the heterologous SerRS from the archaeonMethanopyrus kandleri. The bacterial tRNASec assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNASecs,A. aeolicustRNASec has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs.Methanopyrus kandleriSerRS exhibited serine ligation activity towardA. aeolicustRNASecin vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNASec. Similar interactions exist in the reported tRNASer and SerRS complex structure from the bacteriumThermus thermophilus. Although the catalytic C-terminal domain ofM. kandleriSerRS lacks interactions withA. aeolicustRNASec in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNASec to enter the SerRS catalytic site.