Viability analysis of stored seeds before sowing has a great importance as plant seeds lose their viability when they exposed to long term storage. In this study, the potential of Fourier transform near infrared spectroscopy (FT-NIR) was investigated to discriminate between viable and non-viable triploid watermelon seeds of three different varieties stored for four years (natural aging) in controlled conditions. Because of the thick seed-coat of triploid watermelon seeds, penetration depth of FT-NIR light source was first confirmed to ensure seed embryo spectra can be collected effectively. The collected spectral data were divided into viable and nonviable groups after the viability being confirmed by conducting a standard germination test. The obtained results showed that the developed partial least discriminant analysis (PLS-DA) model had high classification accuracy where the dataset was made after mixing three different varieties of watermelon seeds. Finally, developed model was evaluated with an external data set (collected at different time) of hundred samples selected randomly from three varieties. The results yield a good classification accuracy for both viable (87.7%) and nonviable seeds (82%), thus the developed model can be considered as a "general model" since it can be applied to three different varieties of seeds and data collected at different time.