The scorpions, named Mesobuthus martensii, commonly called Quanxie (全蝎) in Chinese, have been widely used as one of the animal medicines for more than 1,000 years because of the strong toxicity of their venoms. Meanwhile, scorpions are sexually dimorphic in appearance, and many exhibit traits associated with sex-biased gene expression, including maternal care, mating competition, female mating choices, ecology, and even venom composition and lethality. This study aims to explore the differences in composition of the venom of scorpions of different sex using the method of transcriptomics. Whole de novo transcriptomes were performed on the samples of M. martensii captured from Gansu Province to identify their sex-biased gene expression. The conserved CO-1 sequences of the captured samples matched that of M. martensii. A total of 8,444 (35.15%), 7,636 (31.78%), 8,510 (35.42%), 7,840 (32.63%), 9,980 (41.54%), and 11,829 (49.23%) unigenes were annotated with GO, KEGG, Pfam, Swissprot, eggNOG, and NR databases. Moreover, a total of 43 metalloproteases, 40 potassium channel toxins, 24 phospholipases, 12 defensins, 10 peroxiredoxins, 9 cysteine proteinase inhibitors, 7 serine protease inhibitors, 6 sodium channel toxins, 2 NDBPs, 1 calcium channel toxin, 1 waprin-like peptide, 1 antibacterial peptide, 1 antimicrobial peptide, and 1 anticoagulant peptide were screened out. With the fold change of 2 and 0.5,
p
value < 0.01, and q value < 0.05 as thresholds, a total of 41 out of 157 (26.11%) toxin-related unigenes had significant differential expression, and this ratio was much higher than the ratio of differentially expressed unigenes out of all annotated ones (8.84%). Of these differentially expressed toxins, 28 were upregulated and occupied the majority, up to 68.30%. The female scorpions showed more upregulated unigenes that annotated with toxins and had the potential to be used as more effective therapeutic drugs. In addition, this method of omics can be further used as a useful way to identify the difference between female and male toxic animals.