Fourier transform infrared (FTIR) microspectroscopy technology is the combination of the FTIR spectrometer and the microscope. This technology is of simple preparation of the samples, can be used in micro-area analysis and micro-samples, and reflect the nature of the samples spectra. Panax ginseng include mountain cultivated ginseng (MCG), garden cultivated ginseng (GCG) and mountain wild ginseng (MWG), but the excavation of MWG is prohibited in China. So, only MCG and GCG were collected and recorded in Chinese pharmacopoeia. In this study, we developed a discriminant analysis (DA) method for recognition of MCG and GCG using FTIR microspectroscopy technology. Twenty MCG samples and twenty four GCG samples were obtained, and their spectra of IR microspectroscopy were collected. Then 33 samples were randomly selected into calibration set and the remaining 11 of the samples were selected into validation set. The authors optimized the pretreatment method, the principal components, the modeling region and the scanning parts when developing the models. The optimized model of discriminant analysis was developed using the pretreatment multiplicative scatter correction (MSC)+Savitzky-Golay filter (SG) smoothing, the region 3 932.14～669.18 cm-1, 4 principal components and the rhizome part. The accuracy of the optimized model got up to 100%. The result demonstrated that infrared microspectroscopy technology combined with DA is of simple operation, rapid, nondestructive and effective, and can be applied to recognize MCG and GCG.