The “Beihong agate” from Heilongjiang province and the “Nanhong agate” from Liangshan (Sichuan province) and Baoshan (Yunnan province) are the most common gem quality red agate in the jewelry market of China. However, few researches have been performed to differentiate theirprovenance. In this paper, 73 red agate samples from three different areas were investigated by chromaticity, Raman spectrum and X-ray diffraction (XRD) to obtain their chromaticity, mineralogy and spectra characteristics. The results show that the “Beihong agate” is mainly composed of α-quartz and moganite, with minor amount of goethite and hematite responsible for the agate’s red color. The mineral phase composition of the “Nanhong agate” is α-quartz with hematite, goethite, calcite and moganite as auxiliary minerals. The domain wavelength of “Beihong agate” ranges from 574 to 605 nm and is concentrated at ［580, 590］ interval, which accounts for yellow to orange tune. In the CIE1976Lab color space, “Beihong agate” shows a≤6.2 and b≤6.3 characteristics. The domain wavelength of “Nanhong agate” from Sichuan province ranges from 589 to 624 nm, while “Nanhong agate” from Yunnan provinceranges from 589 to 599 nm, both are concentrated at ［590, 600］ interval with orange to orange-red tune, and the majority of samples are a>6.2 or b>6.3 in the CIE1976Lab color space. Generally, “Nanhong agate” exhibits deeper red tone, higher chromaand brightness appearance than “Beihong Agate”. In Raman spectra, the peak near 501 cm-1 of the Si—O—Si symmetry stretching and bending vibration in “Beihong agate” is stronger than those in “Nanhong agate”. The results of peak intensity ratio (I501/I463) consistent with the results of area ratio (A501/A463) . Thepeak intensity ratio (I501/I463) and area ratio (A501/A463) measured by powder method are located in the results measured by random points method. Compared with powder method, random points method does not require destruction of samples. Therefore, random points method is suitable for agate’s qualityanalysis. The peak area ratio (A501/A463) of “Beihongagate” is stable from 0.15 to 0.36, while “Nanghong agate” is stable from 0.00 to 0.08. We hypothesize that “Nanhong agate” have experienced a strong dehydration and recrystallization progress after the formation of primary agate, which caused the transformation of moganite intoα-quartz. The comprehensive utilization of chromaticity characteristics, Raman spectra and the peak intensity ratio (I501/I463) or area ratio (A501/A463) can be used to distinguish “Beihong Agate” from “Nanhong Agate”, which is also important to the identification ofagate’s origin and the tracing of unearthed relics.