In this study, eight inbred maize lines with high or low tolerance to cold temperature were investigated using bulk segregant analysis (BSA). Genetic diversity and genetic relationships were investigated using 100 simple sequence repeat (SSR) markers linked to cold tolerance in maize. A total of 319 alleles were identified. Among these, 128 were high coldtolerant-specific alleles and 61 were poorly coldtolerant-specific alleles, while the remaining 130 were shared between the two types. The number of alleles per locus ranged from 2 to 5, with an average of 3.19. The major allele frequency varied from 0.39 to 0.53 with an average of 0.47. The average gene diversity and polymorphic information content among all lines were 0.63 and 0.58, respectively. A dendrogram analysis identified three main clusters and most of the high tolerant inbred lines were clearly distinguished from the poorly tolerant inbred lines. In addition to the BSA, a total of 84 SSR markers were identified as high cold tolerance-specific alleles and 52 SSRs were detected as poorly cold tolerance-specific alleles. Of these, bnlg1273, umc1124, dupssr21, mmc0251, mmc0181, and phi041 have great potential for being molecular markers for cold tolerance in maize. Our results were in agreement with results previously reported for SSR markers linked with cold tolerance in maize. The identification and characterization of high and poorly cold tolerant maize lines based on SSR markers will be useful for future maize breeding studies.