Identification of quantitative trait loci (QTLs) and their causal genes that govern diverse agronomic traits in crop populations is important for efficient and rapid breeding via markerassisted selection. In rice, many QTLs or genes have been reported for heading date, plant architecture, grain size and number, etc. However, the diversity of these traits present in real varieties far exceeds the variation explained by the accumulation of the known genes. For this reason, the fine-tuning of quantitative traits using genome information is still limited. Our previous genome-wide association study using temperate japonica rice varieties suggested that the old varieties could have novel and unique alleles for higher yield and lodging resistance. To identify such alleles, we selected and crossed two varieties with significantly different traits that could not be explained by the known genes. One is 'Kameji', a landrace selected out about 150 years ago. 'Kameji' has long and thick culms and large panicles. The other is 'Nakate-Shinsenbon', an old variety bred about 70 years ago. 'Nakate-Shinsenbon' has short and thin culms and shows high tillering. The QTL analysis using recombinant inbred lines derived from crossing 'Kameji' and 'Nakate-Shinsenbon' revealed novel QTLs associated with heading date, culm length and culm thickness. Among them, qDTH10, a novel QTL for heading date, had an additive effect of 4.5 days and was considered to be the major QTL determining the difference between the two varieties. For the culm length, a total of five QTLs were detected on chromosomes 1, 2, 4, and 12, all of which 'Kameji' alleles lead to long culms. qCL12, which had the largest effect, was highly associated with first and second internode elongation. On the other hand, the other four QTLs were associated with lower internode length. We also detected QTLs with pleiotropic effects on culm thickness, spikelet number and panicle number on chromosomes 5 and 7. Although these were detected by other genetic analyses, the causal genes have not been elucidated. These unutilized alleles in old varieties can be useful for responding to the diversification of breeding needs and global environmental changes.