Pinus yunnanensis Franch . , P. kesiya var. Langbianensis and P. densata Masters have take n on an obvious geographical overlapped region and were difficult to be dis tinguished . In this study, w e discriminated these three species by Fourier transform near infrared (FT - NIR) spectroscop y . The discriminant analysis model incorrectly assessed the P. kesiya to P. yunnanensis species in cross areas , and optimized one was able to estimate the unknown samples exactly while the overlapped P. kesiya in dividuals have been abandoned , which highly matched the geographical distribution of P. yunnanensis , P. densata and P. kesiya . T he close relationship between P. yunnanensis and P. kesiya probably resulted from the gene flow among species in cross areas .