Oilseeds and their products are the most valuable agricultural crops in world trade. Canola includes the yellow and the black-seeded varieties. Apart from the chemical composition of oilseed crops, their protein secondary structure profiles may also influence protein quality, nutrient utilization and availability. Although data are rare, is vital to study protein secondary structure to understand crop’s digestive behavior and nutritional value. A new approach is the use of Fourier-transformed infrared-vibration spectroscopy (FT/IR), a technique for studying the secondary structural composition, stability and conformational changes. The objective was to evaluate the nutritive value of canola seed, for ruminants, in terms of: 1) chemical and nutrient profiles 2) rumen degradation kinetics, 3) in vitro intestinal protein digestibility and 4) protein molecular structures. Yellow (CS-Y) and black (CS-B) canola seeds (n = 4) were collected from 2 harvest years (2010, 2011) and used as feed sources. Three dry Holstein cows fitted with rumen cannula were used in an in situ trial; then a 3-step in vitro procedure was conducted to determine protein intestinal digestibility. CS-Y was lower in nitrogen detergent fiber and acid detergent fiber (P < 0.05). Crude protein content was not different between the 2 varieties but the non-protein nitrogen was lower (P < 0.05) for CS-Y compared with CS-B. The net energy for lactation, the digestible and metabolisable energy were higher (P < 0.05) for CS-Y compared with CS-B. The C20:1 eicosaenoic acid content (n-9) was lower (P < 0.05) while the total polyphenols were tended to be lower (P ≤ 0.10) for the CS-Y than for the CS-B. No significant differences were observed for the effective degradability of protein and the protein’s inherent molecular structural make up, between the CS-Y and the CS-B. The in vitro protein intestinal digestibility of CS-Y was higher (P < 0.05) compared with that of CS-B. In conclusion, the breeding of CS-Y has the potential to be a promising route to reducing fiber and hull content, while at the same time increasing the level of oil.