Rice cold tolerance is an important breeding target, particularly for Tongil-type rice. In this study, six molecular markers were developed for cold tolerance-related genes using five rice cultivars. dCAPS markers targeted OsCTK1 and OsSAPK6, tetra-primer ARMS-PCR markers targeted COLD1, LTG1, and HAN1, and a KASP marker targeted OsLUX. The markers discriminated allelic variation among cultivars. COLD1, LTG1, and HAN1 markers targeted characterized functional polymorphisms, whereas OsCTK1 targeted a haplotype-linked SNP and OsSAPK6 and OsLUX targeted parental polymorphisms. These markers may facilitate parental allele tracking and marker-assisted selection for cold-tolerance breeding in rice.