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Transcription factor (TF) families play important roles in plant stress responses. <i>S. caninervis</i> is a new model moss for plant desiccation tolerance studies. Here, we report a high-confidence identification and characterization of 591 TFs representing 52 families that covered all chromosomes in <i>S. caninervis</i>. GO term and KEGG pathway analysis showed that TFs were involved in the regulation of transcription, DNA-templated, gene expression, binding activities, plant hormone signal transduction, and circadian rhythm. A number of TF promoter regions have a mixture of various hormones-related <i>cis</i>-regulatory elements. AP2/ERF, bHLH, MYB, and C2H2-zinc finger TFs were the overrepresented TF families in <i>S. caninervis</i>, and the detailed classification of each family is performed based on structural features. Transcriptome analysis revealed the transcript abundances of some Sc<i>AP2/ERF</i>, <i>bHLH</i>, <i>MYB</i>, and <i>C2H2</i> genes were accumulated in the treated <i>S. caninervis</i> under cold, dehydration, and rehydration stresses. The RT-qPCR results strongly agreed with RNA-seq analysis, indicating these TFs might play a key role in <i>S. caninervis</i> response to abiotic stress. Our comparative TF characterization and classification provide the foundations for functional investigations of the dominant TF genes involved in <i>S. caninervis</i> stress response, as well as excellent stress tolerance gene resources for plant stress resistance breeding.