Shirakawa-ishi is a famous granite that in the past was widely used for gardening and construction. The Shirakawa-ishi quarrying industry in northern Higashiyama was famous for the high techniques of the stonecutters of Kyoto. However, after having been closed for over a half century, the Shirakawa-ishi quarries now remain forgotten. This study aimed at recovering the location and transition of Shirakawa-ishi quarries in modern times, and summarizing the components and geographical features of Shirakawa-ishi quarrying sites. We collected and analyzed information on Shirakawa-ishi quarrying sites from documents, surveys, and old topographic maps, then conducted field investigations with GPS and the newest topographic maps. 4 quarrying areas (south Uryuyama, Yamanakagoe, Otowagawa, and south Shimeigadake) were recovered. The quarrying sites were closed no later than 1966 after the prosperous period from the Meiji era to the early Taisho era. Components of quarrying sites including rock cliffs in valley sides, flat working fields, stacked stones, and export routes were confirmed. Quarry searching based on the distance from the village, rock selection and export route choice in consideration of geographical features and existing mountain trails, and topography improvement by stacked stone design showed valuable traditional intelligence in natural resource use.