show Abstracthide Abstractdistribution of organisms was formed from the past is an essential issue in evolutionary ecology. Recently, the distribution of organisms on Earth has been significantly changed by human-mediated dispersal with globalization. Therefore, significant attention has been paid to such processes. However, although humankind had taken considerable time to achieve modernization, the impact of ancient human activity on ecosystems had not yet been thoroughly studied. We hypothesized that ancient urban development and transitions had a non-negligible effect on species distribution.Considering that Schlegel's Japanese gecko, Gekko japonicus, one of the popular neighbors of human dwellings in Japan, is a good model for this, we sequenced these genes. By analyzing these sequence data, we clarify the history of the origin and dispersal of G. japonicus in the Japanese archipelago, showing that ancient human-organism interactions can be an essential factor in understanding the present distribution of organisms.