Abstract: Objective To compare the sensitivity and reproducibility of Allglo and TaqMan probe in the detection of simian immunodeficiency virus (SIV) using fluorescence quantitative RT-PCR (QPCR). Methods The reference sample of SIV was diluted to 6 gradient concentrations; at each concentration 12 samples were tested to analyze the variations within batches, and each sample was tested for 12 times for analysis of variations between batches by QRT-PCR using TaqMan probe and Allglo probe. The results of QPCR using the two probes were analyzed with ABI7300 PCR system software. Results In QPCR using TaqMan and Allglo probe, the lower limit of sensitivity for SIV detection was both 50 copies/mL. Assessment of the reproducibility of the tests showed that the maximum and minimum coefficients of variation between batches were 0.63% and 0.33 % with Allglo probe, respectively, as compared with 1.33% and 0.2% with TaqMan probe. The maximum and minimum coefficients of inter-batch variation was 1.77% and 0.95% with Allglo probe, respectively, as compared with 1.86% and 1.03% with TaqMan probe. Conclusion Allglo probe shows a better performance then TaqMan probe in detection of SIV QPCR.