Koshu is indigenous to Japan and considered the most important wine grape in Japan. Koshu grape berry possesses characteristics that make it unique from European V. vinifera as wine grape. However, the physiological characteristics of Koshu leaf and internode remain unknown. An understanding of those characteristics would contribute to improvements in Koshu cultivation, thereby enhancing grape berry and wine quality. To identify the genes responsible for the physiological characteristics of Koshu, we comprehensively analyzed leaf and internode differences at the transcriptome level between Koshu and Pinot Noir by RNA sequencing. A total of 248 and 131 differentially expressed genes (DEGs) were detected in leaves and internodes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of these DEGs revealed that "flavonoid biosynthesis" and "glutathione metabolism" pathways were significantly enriched in Koshu leaves. On the other hand, when internodes were compared, "flavonoid"-related GO terms were specifically detected in Koshu. KEGG pathway enrichment analysis suggested that the expression of such genes as leucoanthocyanidin reductase and flavonol synthase in the flavonoid biosynthesis pathway was higher in Koshu than Pinot Noir. Measurement of the relative expression levels of these genes by RT-qPCR validated the results obtained by RNA sequencing. The characteristics of Koshu leaf and internode, which are expected to produce flavonoids with antibacterial activity and UV protection function, would suit Japanese climate as a survival strategy.