Variants of the rodent vesicle-associated membrane protein 1 gene (VAMP1) play a key role in resistance to botulinum neurotoxin type D (BoNT/D) rodenticide. In this study, we analyzed the VAMP1 gene in five species of rodents, which are endemic to the Qinghai-Tibet Plateau, using transcriptomic methods: Plateau Pika (Ochotona curzoniae), Plateau Zokor (Eospalax baileyi), Lesser Long-tailed Hamster (Cricetulus longicaudatus), Plateau Vole (Neodon fuscus) and Himalayan Marmot (Marmota himalayana). We sequenced the transcriptome of the brain of each species using Illumina HiSeqTM 2000 platform. We then assembled the reads using Trinity program, extracted the VAMP1 coding sequence using blastn program, and finally analyzed their genetic variations using DNAstar and MEGA programs. We also sequenced the second exon of VAMP1 gene of 58 plateau pikas and 59 plateau zokors from five geographical populations using Sanger sequencing methods (Table 1) and analyzed the sequence variations among individuals using MEGA program. We successfully obtained the complete coding sequences of VAMP1 gene of the five QTP animals from transcriptome assemblies. The VAMP1 sequences of all five animal species were 357 bp in length. There were 46 variable sites at the DNA sequence level and four variable sites at the amino acid sequence level among the five Qinghai-Tibet Plateau animals (Table 2, Fig. 1). None of the amino acid residues was identical to that involved in BoNT/D resistance in other animals. We did not detect any variable sites in the second exon of VAMP1 gene of the 58 pikas, and only one synonymous mutation among the 59 zokors was found. Again, we did not detect any BoNT/D resistance mutants in the pikas and zokors. Our study suggests that these rodent species are unlikely to develop resistance to BoNT/D. Based on our results coupled with scientific guidance on usage, the BoNT/D rodenticide can be potentially used in rodent control in the Qinghai-Tibet Plateau.