In most Old world monkey species, TRIM5α plays a role in combating retroviruses and restricting HIV-1. Alongside TRIM5α, the TRIMCyp fusion gene formed by the retrotransposition of a CypA pseudogene cDNA to 3' terminal or 3'-UTR of TRIM5 gene in these monkeys has become a key research area in anti HIV-1 factors. The regional differences, gene frequencies, genotypes, and retrovirus restrictive activities of TRIMCyp vary among different primate species. While the frequencies of cynomolgus TRIMCyp have been studied in several areas of Southeast Asia, the frequency and prevalence of cynomolgus TRIMCyp in China remains unclear. In this study, we screened 1, 594 cynomolgus samples from 11 monkey manufacturers located across 5 provinces in China. Our results showed that the frequencies of TRIMCyp range from 7.65% to 19.79%, markedly lower than the frequencies found in monkey species in the Philippines, Malaysia and Indonesia (ranging from 34.85% to 100%). We speculate that potentially the latter were isolated groups established since 1978. The NE haplotype frequencies of cynomolgus TRIMCyp were 4.93% in China, also significantly lower than those found in species in the Philippines, Malaysia and Indonesia (from 11.1% to 14.3%). Our research provides interesting findings that contribute towards a more firm basis of further studies of HIV-1 animal models and relevant pathogenesis.