PCV2e shows high sequence similarity to other PCV2 genotype, causing greater difficulties in the molecular biological identification of pathogens. In this study, we developed a TaqMan-based RT-qPCR for efficient detection of PCV2e in clinical samples. We designed specific primers and a probe for the PCV2e ORF2 gene and then identified target genes using the optimized PCR reaction system and reaction conditions. The results indicated that the cycle threshold (Ct) and the standard DNA template had a linear relationship between 10³-10⁸ copies/µL, and the determination coefficient was 0.998. The assay has a detection limit of 100 copies per reaction and a standard deviation of cycle thresholds below 1.00. The PCR method we established can specifically identify PCV2e, did not cross-react with other genotypes of PCV, as well as PRV and PPV. The RT-qPCR assay can be used for the special diagnosis and epidemiological investigation of PCV2e.