There is growing interest in the use of pine hybrids in commercial forestry plantations in the tropics and sub-tropics. However, the production of pine hybrid seeds can be difficult and is dependent on the presence of an adequate number of male and female strobili, timely application of the pollination bag, good pollination techniques and reasonable weather conditions. After pollination, a wait of two or more years is required for cones to mature and for seeds to be collected. The seeds collected from artificial hybrid crosses in an orchard are assumed to be true hybrids, but might also be the (female) pure species if pollen contamination has occurred prior to or during bagging of the male strobili. Confirming hybridity in pines is often very difficult in the seedling stage when only needle morphological characteristics are used. In this study, we examined ground oven-dried needle samples of 16 pine species from different geographic regions using near infrared (NIR) spectroscopy to determine if this method is effective in distinguishing between pine species. We also created three “simulated hybrids” by manually mixing needles from three sets of parental pure species. The raw near infrared reflectance spectroscopy data were transformed using standard normal variate and de-trending techniques and a model was developed to distinguish between pure pine species and their “hybrids” using discriminant analysis. A total of 120 paired-species models were developed (one for each potential hybrid of the 16 species). For each of the 120 paired-species models, there were 20 independent observations in a validation data set and the 2400 observations were classified with 94% accuracy. Models were also developed for each of six species-simulated hybrid data sets. A total of 120 independent validation observations were classified as either parental species or simulated hybrid with 90% accuracy. The results indicate that NIR spectroscopy can be used as an effective tool to distinguish between pure pine species and suggest that it will also distinguish hybrids from their parents. Using NIR spectroscopy to verify hybridity in pines might be quicker and less expensive and, in some cases, as accurate as using molecular techniques.