Sugarcane is cultivated in tropical parts of the world. Cold stress can damage the crop and cause economic losses. Fundamental studies on gene expression patterns during cold stress can be consulted to better understand the mechanism of cold tolerance. To select the most tolerant and susceptible sugarcane cultivar to cold stress, morphological and biochemical measurements were performed in the field (-1.2°C and 0.6 °C) in two years. In the second year, two cultivars were identified as the most tolerant and susceptible cultivars to cold, respectively. These cultivars were then subjected to -2°C in Cool chamber (6 and 12 hour) for transcriptomic evaluation. The RNA sequencing was performed afterwards. Then, the transcriptome analysis using SUCEST-FUN data base was performed. Results of differential analysis of gene expression showed between expressed 62225 genes after the cold stress, 12674 genes with differential expression. Results of pathway and annotation analysis of gene interpretation showed that the number of genes involved in the Phenylpropanoid biosynthesis pathway (125 genes) and the MAPK signaling pathway (75 genes) in the resistant cultivar was higher than the susceptible cultivar (62 and 38 genes respectively). Meanwhile, PR1 gene was detected in the MAPK messenger pathway, which showed an increase in the expression level with decreasing temperature.