The current real-time PCR (polymerase chain reaction) platforms, which can detect and quantify several target DNA simultaneously, are equipped with discrete optics and detectors for different fluorescence wavelengths. However, the optical loss, due to the different lengths of the channels for several dyes, lowers the performance of fluorescence detection. Especially on the PCR platforms of lab-on-a-system, for the dispersion of the fluorescence in the micro fluidic channels, the received fluorescence is much lower than the emitted. To enhance the received intensity on the detection system is therefore a critical issue. The proposed fluorescence detection system, composing of an ultra-sensitive spectrometer, can provide continuous wavelength detection and can be employed for multiple DNA quantification and genotyping in a single reaction. For the tests to the genotyping ability, the melting temperatures of B type HBV and C type HBV can be distinguished by the difference of 1.1 C.The test results in this research show the same degree of sensitivity for DNA quantification and reproducibility within five intra assay samples as compared with a commercial one.