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The resurrection plant Selaginella pulvinata possesses an extraordinary ability to survive longterm desiccation, with the capacity to recover to normal growth after four years in a desiccated state. To understand the phenomenon, we investigated morphology, cytology, physiology, and performed PacBio single-molecule, real-time (SMRT) sequencing and Illumina RNA-sequencing of S. pulvinata during dehydration and rehydration. The full-length transcriptome dataset of S. puvinata consisted of 78,914 isoforms, and 75,819 isoforms (96.07%) were functionally annotated. The mapping rate of RNA-seq was 86.83–93.46% when utilizing the full-length transcriptome dataset as a reference. A total of 17,934 differentially expressed genes (DEGs) were identified during dehydration and rehydration. During dehydration, swollen chloroplasts and mitochondria, as well as vacuolation occupied space in desiccated cells, which cooperated with dense cytoplasm to inhibit the collapse and folding of desiccated cells. Accumulation and up-regulated gene expressions of osmotic agent and protective proteins contributed to the formation of vacuolation and dense cytoplasm. To reduce ROS damage during dehydration, two strategies were employed in S. pulvinata , i.e., reducing ROS production and scavenging ROS. Reducing exposure area, inactive PSII and down-regulated gene expression in photosynthesis decreased ROS production caused by excessive light absorption. Increased activities and up-regulated gene expressions in antioxidant enzyme system promoted ROS scavenging. ABA signaling pathway was hypothesized to play an important regulatory role in the desiccation tolerance of S. pulvinata due to significant ABA accumulation and up-regulated expressions of related genes during dehydration. Moreover, the comparative transcriptome analysis revealed that the pathways involved in dehydration and rehydration of the resurrection species S. pulvinata , S. lepidophylla and S. sellowii were consistent, indicating the similar desiccation tolerance mechanisms existing in the different resurrection species of Selaginella. Our study preliminarily revealed the desiccation tolerance mechanisms of S. pulvinata , which holds significant potential for inspiring biotechnological strategies aimed at enhancing drought tolerance in crops. • Changes of morphology, physiology, cytology and transcriptome level were observed in S. pulvinata during dehydration and rehydration. • Desiccation tolerance of S. pulvinata was an intricate process orchestrated by many genes and metabolic pathways. • The different resurrection species of Selaginella possessed the similar desiccation tolerance mechanism. [ABSTRACT FROM AUTHOR]