Due to depletion of the stratospheric ozone layer throughout most of this century, increased UV-B radiation has affected seriously to plant growth and development as one of nature mutagens. We surveyed differential expressed genes (DEGs) under UV-B irradiation in UV-B tolerant Buseok compared to UV-B sensitive Cheongja 3 through RNA seq analysis using six RNA samples of Buseok and Cheongja 3 with 0.5 hr and 6 hr UV-B irradiation or without irradiation. After excluding 1003 DEGs due to genetic background difference of two genotypes, a total of 872 DEGs orthologous to UV-related Arabidopsis genes were identified. BINGO analysis of the DEGs by 0.5 hr UV-B irradiation showed overrepresentation in signaling and cell morphogenesis. Genes related with apoptosis and immune response were overrepresented in 6 hr irradiated Buseok. In addition, KEGG pathway database was used to identify mTOR signaling and phosphatidylinositol signaling pathways. Based on GO and KEGG results, specific focus was given to a serial of genes involved in UV-B defense signaling, besides photomorphogenesis and oxidation reduction-related genes. Several genes playing a role in phosphatidylinositol signaling, such as diacylglycerol kinase, phosphatidylinositol-4-phosphate 5-kinase family protein, were highly expressed in UV-B tolerant Buseok by 0.5 hr irradiation. Mitogen-activated protein kinase (MAPK) 19 and 20 were highly expressed in Buseok under 6 hr irradiation. Furthermore, 51 nucleotide binding site leucine rich repeats (NBS-LRRs) genes were up-regulated in Buseok under 0.5 hr irradiation.