We studied the morphological differences among breeding populations of the Arctic Warbler Phylloscopus borealis across the Far East and Alaska. We previously identified three strong monophyletic clades of the Arctic Warbler based on molecular phylogeny using mitochondrial DNA (cytochrome b): Clade A (Alaska, Anadyr, and Magadan), Clade B (Kamchatka, Sakhalin, and Hokkaido), and Clade C (Honshu, Shikoku, and Kyushu). To identify whether there are external morphological differences among these three mitochondrial clades, we used canonical discriminant analysis (CDA) and principal component analysis (PCA). CDA showed that the morphological differences among populations corresponded well with each mtDNA clade, with classification accuracies of 94.55%. In particular, populations of Clade C differed distinctly from Clades A and B in their longest natural wing and P10-PC lengths. The measurements of Clades A and B partly overlapped. In contrast, PCA enabled us to identify all individuals of each population correctly. Arrangement of populations in order of body size based on PC1 were Honshu>Kamchatka>Hokkaido/Sakhalin>Magadan/Alaska. We also found a latitudinal trend in body size and P10-PC lengths, which became smaller with increasing latitude. This trend in body size provides an example of reversed Bergmann's rule in birds. The latitudinal trend of P10-PC lengths may be related to migration distance. Our morphometric analyses suggest that the Japanese subspecies P. b. xanthodryas (Honshu and Kyushu) is readily identifiable based on measurements, whereas although the subspecies P. b. examinandus and P. b. borealis/kennicotti are also identifiable, some individuals of the latter two clades are similar in morphology.