The identification of Nanfeng mandarins from different origins was developed by using near infrared spectroscopy (NIR) and principal components analysis (PCA). Mandarins from different places in one orchard, and from different orchards in three towns of Nanfeng county were studied. Also differences among Shaowu, Liucheng and Nanfeng were investigated. Furthermore, the effect of storage time of mandarins on the PCA model was considered. The results demonstrate that there was no clear diversity of the mandarins in one origin but great differences existed among different ones. And the storage time of mandarins played little role in the discrimination model. The method of multiple scattering correction (MSC) coupled with second derivative was selected to build PCA discrimination models compared with other data pretreatment methods. The proposed model would be a reference method for origin identification of Nanfeng mandarin.