Protein phosphatase 2 C (PP2C) gene family is known for regulating a variety of abiotic stresses in plants. However, little is currently understood about this gene family in jute. In this study, a total of 60 CcPP2C genes were identified in jute, which were named from CcPP2C1 to CcPP2C60 according to the order of their physical coordinates. These CcPP2C proteins contained about 162–1324 amimo acids. Their isoelectric points varied in the range of 4.51–9.45, and their molecular weights varied from 18.307 to 146.906 kDa. The evolutionary tree of PP2Cs in jute and Arabidopsis indicated that PP2Cs can be divided into 12 branches. Sixty-seven collinear gene pairs were identified between 42 CcPP2Cs and 62 AtPP2Cs by analyzing the whole genome collinearity data of jute and Arabidopsis. The analyses of conserved motifs in these CcPP2C proteins and cis-elements in the promoters revealed that CcPP2Cs might play an extensive role in responses to various abiotic stresses in jute. Particularly, the expression patterns of CcPP2Cs in group A under salt treatments showed that CcPP2C51 was up-regulated under various stress treatments. And CcPP2C51 was localized in the nucleus and cell membrane. In Arabidopsis, the overexpression of CcPP2C51 positively regulated the salt-tolerance genes. Also, the overexpression of CcPP2C51 improved the salt tolerance of jute regenerated roots. This study revealed the origin and evolution of PP2C genes in jute, and provides potential possibilities for molecular breeding of jute. Display omitted •A total of 60 CcPP2C genes were identified in jute•These 60 CcPP2C genes are evolutionarily conserved and might be involved in stresses•Different expression patterns were observed under salt treatment in CcPP2Cs•CcPP2C51 was found to be localized in the nucleus and cell membrane•Overexpression of CcPP2C51 in Arabidopsis and jute resulted in salt tolerance