Zooarchaeology is the branch of archaeology that helps reconstruct the human past using animal remains from archaeological sites. These remains are also useful for reconstructing the palaeoecology of animals. In Japan, although several archaeozoological studies have focused on temporal changes in the size and distribution of mammalian species, there have been few archaeornithologial investigations of bird species. More than 600 avian species, with diverse ecological traits, have been recorded in Japan. Various responses to temporal environmental changes are thought to have occurred throughout the evolutionary history of birds; thus, we expect to find different ecological adaptations in birds to those seen in mammals. The identification and morphological, histological, genetic, and geochemical analyses of bird bones reveal several aspects of their palaeoecology, such as their distribution, morphology, population structure, genetic diversity, and food habits. Archaeornithological research on the Short-tailed Albatross Phoebastria albatrus revealed that the species was once distributed in the northern part of the Sea of Japan and the southern part of the Sea of Okhotsk. Furthermore, results show that there were two distinct albatross populations, with differing body sizes and food habits, about 1,000 years ago, and that the descendants of these populations now live on Torishima and Senkaku islands, respectively. Such findings provide essential information for directing conservation policy for this vulnerable seabird, which might in fact consist of two species. Whole genome analyses, using next generation sequencing, and collagen peptide identification will be applied to the analysis of archaeological bird bones to further archaeornithological research. Ornithological research has advanced mainly with regard to evolutionary and ecological time scales. Information obtained via archaeornithological research fills the gap between these time scales, making this field as valuable in Japan as it is elsewhere.