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DNA methylation plays an indispensable role in genome stability, regulation of gene expression and plant stress response. It is mediated by DNA methyltransferases (MTases). Twelve putative MTases of <i>P. betulaefolia</i> were identified and were classified into MET1, CMT, DRM2 and Dnmt2 groups based on the organization of various characteristic domains. Three pairs of paralogous genes were identified with the <i>K</i>a/<i>K</i>s ratio varied from 0.232 for <i>PbeMET1a</i> and <i>PbeMET1b</i> to 0.251 for <i>PbeCMT2</i> and <i>PbeCMT3</i>, respectively. In addition, the <i>K</i>a/<i>K</i>s ratio for nine pairs of orthologous gene pairs between <i>P. betulaefolia</i> and apple were varied from 0.053 for <i>PbeDRM3</i> and <i>MD17G1031900</i> to 0.278 for <i>PbeDnmt2b</i> and <i>MD15G1120500</i>, respectively. All the 12 members of MTase genes were located on nine chromosomes out of 17 <i>P. betulaefolia</i> chromosomes with highly conserved protein sequence structures. The isoelectric points (pI) of MTases ranged from 4.74 to 7.24, while molecular weight varied from 35.99 to 174.32. The expression profiles of MTase and other salt-responsive genes under salt stress treatment revealed their important roles involved in salt response in <i>P. betulaefolia</i>. Furthermore, three selected salt-responsive genes (<i>PbeNHX2.1</i>, <i>PbeCBL2</i> and <i>PbeAKT2</i>) were found altered in methylation level of promoters (which contain CpG islands) under salt stress. Especially, the <i>PbeAKT2</i> promoter regions showed high CHG and CHH methylation types. Our study provided a genome-wide survey of the MTase gene family and highlighted their roles in salt response. These results also provided an effective way for the breeding and improvement of salt-tolerant pear varieties.