Objective To study the impact of cSNP on the structure and function of samhd1 gene in rhesus macaques. Methods RNA was extracted from peripheral blood of rhesus macaques. The cSNP sites were detected and confirmed through reverse transcription PCR, sequencing and sequence alignment. Protein structure and function were analyzed with Predictprotein and SWISS-MODEL. Finally, the functional cSNP sites were screened by SNaPshot technique in a larger sample scale. Results Five non-synonymous mutation sites (C15G (2.17%), C320T (6.88%), G547A (13.41%), A552T (4.35%) and T839C (17.39%)) were found, respectively. Four of them, except C15G, were included in the key structure domains of SAMHD1. Meanwhile, G547A, A552T, T839C had secondary structure changed and were likely to impact the function of SAMHD1. Conclusion Some important cSNP sites are found in samhd1 gene of rhesus macaques, which may impact on the function of SAMHD1.