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[Aim] Tenebrionid insect Microdera punctipennis is an endemic species in Gurbantunggut Desert, Xinjiang, China. It has very strong cold hardiness, but the molecular mechanisms by which M. punctipennis responses to low temperature are still unclear. This study aims to enrich the genetic information of M. punctipennis, and to analyze the functional groups of the most up-regulated genes under short-term cold stress and the pathways which they may involve in. [Methods] Transcriptomic sequencing reads from M. punctipennis adults exposed to 4[degrees]C as low temperature treatment and 25[degrees]C as the control, respectively, for 3 h were de novo assembled by using Trinity software. Gene annotation was conducted by using Blast2go software. The differentially expressed genes were screened by using DESeq and GFOLD softwares. For the up-regulated genes, GO term enrichment and KEGG metabolic pathway analysis were performed using Blast2go software. [Results] In total, 51 712 non-redundant transcripts with the average length of 984 bp were assembled, of which the expression levels of 514 genes were up-regulated and 91 genes down-regulated in response to cold stress. The up-regulated ones were enriched to 35 GO terms and 18 KEGG pathways, showing that stress-related GO terms, biological regulation and immune system are enriched significantly. Pathways such as purine metabolism, thiamine metabolism, and glycolysis/gluconeogenesis are significantly enriched. In the stress responsive GO term, the expression levels of eight abiotic related genes, including heat shock protein (Hsp90) gene, superoxide dismutase (SOD) gene, calnexin gene, etc., were up-regulated significantly. [Conclusion] The transcriptomic data of the desert beetle M. punctipennis reveal that the expressions of genes related to the biological processes like metabolic process, stress response, biological regulation and immune system are significantly up-regulated during cold acclimation at 4[degrees]C. The metabolic pathways revealed by KEGG enrichment show that low temperature transcriptome of M. punctipennis is much different from those of other species. Our results provide basic data for successive bioinformatics analysis and mining the key genes in cold tolerance for M. punctipennis as well as for elucidation of the related molecular mechanisms.