Low temperature germinability (LTG) is an important trait for breeding of varieties for use in direct-seeding rice production systems. Although rice (Oryza sativa L.) is generally sensitive to low temperatures, genetic variation for LTG exists and several quantitative trait loci (QTLs) have been reported. The objective of this study was to develop and employ high-efficiency molecular markers for evaluation of LTG in rice germplasm. A panel of japonica rice accessions (n=180) from temperate regions in Asia was evaluated for LTG and genotyped with markers from regions previously reported to harbor other LTG QTLs. ANOVA revealed that four markers on chromosome 2, 4, and 11 from previously reported QTLs showed highly significant value (p < 1.0e-04) and their R2 ranged 0.083 (qLTG11-1) to 0.190 (qLTG4b-1). An association analysis was conducted using SNP data generated by sequencing of the panel. Eight SNP markers were found to be significantly associated with LTG using general and mixed linear models. Three SNP-based CAPS and dCAPS markers from these results were developed and showed higher accuracy in predicting sensitive LTG germplasm. These new LTG markers will be useful for molecular evaluation of germplasm, particularly to identify sensitive or weak LTG accessions.