Waxy proteins play a key role in amylose synthesis in wheat. Eight lines of common wheat (Triticum aestivum L.) carrying mutations in the three homoeologous waxy loci, Wx-A1, Wx-B1 and Wx-D1, have been classified by near-infrared (NIR) and Raman spectroscopy combined with chemometrics. Sample spectra from wheat seeds were collected by using a NIR spectrometer in the wave rage 1600–2400 nm, and then Raman spectrometer in the wave range 700–2000 cm^–1. All samples were split randomly into a calibration sample set containing 284 seeds (∼35 seeds per line) and a validation sample set containing the remaining 92 seeds. Classification of these samples was undertaken by discriminant analysis combined with principal component analysis (PCA) based on the raw spectra processed by appropriate pre-treatment methods. The classification results by discriminant analysis indicated that the percentage of correctly identified samples by NIR spectroscopy was 84.2% for the calibration set and 84.8% for the validation set, and by Raman spectroscopy 94.4% and 94.6%, respectively. The results demonstrated that Raman spectroscopy combined with chemometrics as a rapid method is superior to NIR spectroscopy in classifying eight partial waxy wheat lines with different waxy proteins.