The chestnut (genus Castanea) has a long juvenile phase, and breeders have to wait three years or more to evaluate nut traits. Therefore, molecular markers associated with genes of interest are required to speed the selection process in chestnut breeding programs. Genetic linkage maps of the Japanese chestnut were constructed using two breeding populations derived from crosses between ‘Kunimi’ and breeding line ‘709-034’ (Kx709), and between ‘Porotan’ and ‘Tsukuba-43’ (Px43). Maps of the four parents and two integrated maps (one representing each cross) were constructed using 443 simple sequence repeat markers (SSRs) and 554 single-nucleotide polymorphism markers. In the Kx709 integrated map, which was the most saturated of the six maps, 12 linkage groups were identified that covered 668.1 cM with an average distance of 0.8 cM between loci. Using anchor SSRs, these six maps were successfully aligned to the Chinese chestnut consensus map. We evaluated eight important traits, including several nut traits, to identify molecular markers associated with these traits. At least one significant quantitative trait locus (QTL) was detected for each of the eight traits (21 in total). Logarithm of odds (LOD) values and phenotypic variance explained by these QTLs ranged from 2.60 to 7.90 and from 11.6% to 29.1%, respectively. In the Kx709 population analysis, several QTLs for nut harvesting date (HARVEST) and pericarp splitting (SPLIT) were detected. Under the assumption that the effects of these QTLs are additive, the percentage of total phenotypic variance explained by the combination of QTLs was high for both HARVEST (47.5%–60.8%) and SPLIT (33.4%–41.7%). Because these mapping populations and their parents are essential materials for Japanese chestnut breeding programs, these QTLs will soon be used for marker-assisted selection to improve breeding efficiency.