We sequenced the complete mitochondrial (mt) genome of
Gavia arctica
. The circular mt genome is 17,065 bp long, consisting of 37 genes (13 proteins, 22 transfer RNAs, and two ribosomal RNAs) and a control region. Phylogenetic analysis based on the full mt genome sequences confirmed that the genus
Gavia
is a monophyletic group, containing the
G. stellata
,
G. arctica
, and
G. pacifica
. These data can provide insights into the phylogenetic relationships for inferring the pattern and degree of mt genome evolution among the loon species.