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Abstract This study applied various scientific analyses to one fragment of paper and three pigments excavated from earthenware found in the Hoeamsa Temple site at Yangju, Korea, which is believed to have been built in the early twelfth century. Radiocarbon dating of the paper fragment suggests a manufacture date between 1460 and 1646 (at a 95% confidence interval). It was estimated to have been used during the early and middle period of the Joseon dynasty (1391–1776), when the Hoeamsa Temple site was rebuilt. In addition, by staining the fiber of the paper fragment with Graff “C” stain, the paper’s raw material was identified as paper mulberry through dislocation, cross-marking, and transparent membrane, which are characteristics of the bast fiber. Efforts were made to identify their material properties and manufacturing techniques of the three types of pigments. Color difference analysis was performed by distributing the pigments in large areas to reveal characteristic differences according to the color difference of the pigment. We found that green-type pigments are malachite and atacamite, red-type pigments are hematite based on the element Fe, and white-type pigments are quartz and muscovite based on the elements Si and Al. In addition, as the size distribution of the three types of pigments is wide and has a multi-peak distribution curve, it was concluded that the pigments were used without purification.