The mechanisms regulating the content ratio of unsaturated fatty acid in sesame oil need to be clarified in order to breed novel varieties with high contents of unsaturated fatty acids. Full-length cDNA libraries prepared from sesame seeds 1 to 3 weeks after flowering were subtracted with cDNAs from plantlets of 4 weeks after germination. A total of 1545 cDNA clones was sequenced. The functions of novel genes expressed specifically during the early maturation of sesame seeds were investigated by the transformation of Arabidopsis thaliana. Thirteen genes for a transcription factor were identified, four of which were involved in ethylene signaling. Fifty-nine genes, including those for the aquaporin-like protein and ethylene response factor, were analyzed by overexpression in A. thaliana. The overexpression of novel genes and the aquaporin-like protein gene in A. thaliana increased the content of unsaturated fatty acids. The localization of these products was investigated by the induction of the expression vectors for the GFP fusion protein into onion epidermal cells and sesame root cells with a particle gun. As a result, two cDNA clones were identified as good candidate genes to clarify the regulation in the yield and the ratio of unsaturated fatty acids in sesame seeds. Sein60414 (Accession No. LC603128), an intrinsic membrane protein, may be involved in the increase of unsaturated fatty acids, and Sein61074 (Accession No. LC709278) MAP3K δ-1 protein kinase in the regulation of the total ratio of unsaturated fatty acids in sesame seeds.