Absorption of light in the electromagnetic spectrum by plant pigments and other types of molecules produces a unique spectral reflectance signature. The aim of the present study is to assess the use of morphological and hyperspectral remote sensing criteria in taxonomy of flowering plants. The macromorphological characters and stomatographic criteria as revealed with SEM were extracted from 20 species belonging to ten families collected from two wadies in Sinai, Egypt. In addition to the spectral reflectance was measured with ASD field spectroradiometer in the wavelength ranged from 350 to 2500 nm. The optimal wavebands and wavelengths were detected by One Way ANOVA (Tukey’s HSD Post Hoc Analysis) and Linear Discriminate Analysis. The phenetic analysis of morphological and hyperspectral characters were performed using NTsys-PC version 2.02 software. Macromorphological diversity was detected and six types of lamina sculpture as revealed with SEM were recognized. Red (550-750 nm) and NIR (760-1000 nm) spectral zones were the optimal to discriminate the different genera. The unique wavelengths for each genus were identified. Hyperspectral technique was considered as a valuable taxonomic tool for flowering plants and was supported with macromorphological data and stomatography.