—The Spectacled Guillemot (Cepphus carbo) is a seabird endemic to northeastern Asia. It is listed as a “Vulnerable” species in Japan, though little is known of its population status. Population surveys were carried out during 2011–2014 throughout their range in northern Japan. Twenty-eight known and six suspected breeding colonies were reported in this region during 1875–2010. Fourteen known and four suspected breeding colonies were found in the 2011–2014 surveys, with 1,169 individuals and 294 nests. Based on our analysis of the two survey periods, 19 colonies have apparently disappeared, and populations have decreased in 12 of the current colonies. Our models indicated that colonies with small numbers of individuals were most likely to disappear, whereas other environmental factors (i.e., colony type, latitude, and SST trends) had relatively minimal effects on local colony extirpation. Our study shows that the population status of the Spectacled Guillemot has deteriorated in Japan.