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Abstract Aim This paper examines body size variation in both recent and Quaternary populations of the Japanese field mouse Apodemus argenteus in order to assess the relative effects on body size of climate change, isolation and competitive interactions with its congeneric A. speciosus. Both temporal (since the Last Glacial Maximum, LGM) and spatial (over the Japanese archipelago) scales are considered. Location The small field mouse is widespread in Japan, and the specimens examined were collected from 10 localities on islands of widely differing area (from 4 km2 to 230,510 km2) and at latitudes ranging from 30.3° N to 45.1° N. Methods The effects of geographical factors such as latitude and island area on the size variation of A. argenteus were investigated, using the lower incisor size. In addition, the size of some specimens from two Quaternary localities was compared with the size of the extant specimens. Evolutionary rates of size change since the LGM were calculated in darwins. Hutchinson size ratios were used to examine the pattern of variation of the size segregation between the two Japanese field mice, A. argenteus and A. speciosus, in relation to time and space. Results There was a negative relationship between size and latitude among living A. argenteus populations. In addition, there was no effect of island area on body size, especially at higher latitudes. At lower latitudes, A. argenteus were larger on smaller islands, although this trend was not statistically significant. Quaternary specimens of A. argenteus were smaller in size than their living representatives. The interspecific size ratio between the two Japanese Apodemus was larger on smaller islands and at higher latitudes, and there has been a decrease in the size ratio between the two Apodemus since the LGM. Lastly, in accordance with the theory of character displacement, the small A. argenteus was larger in allopatry than in sympatry, whereas the large A. speciosus was smaller in allopatry than in sympatry. Main conclusions These results indicate that A. argenteus does not conform to Bergmann's rule or to the island rule. The variation in size for the small Japanese field mouse at both spatial and temporal scales may be related to climate change, with an additional effect of competition with the large field mouse, especially on smaller islands. The size convergence between the two Japanese Apodemus observed over the last 21,000 years may be explained by the diminution of available food resources due to the reduction of land mass areas following the LGM. It may also be the result of an evolution towards an optimal body size; a hypothesis previously proposed to explain the evolution of body size in island mammals. Lastly, the evolutionary rates of body size calculated for A. argenteus since the LGM are typical of rates calculated for other Quaternary mainland mammals, thus suggesting that the evolution in this species was not particularly rapid, as is often thought for island mammals.