Leather produced from crocodile, alligator, and caiman skin is widely used in the fashion industry. Crocodilian leather is generally more expensive than mammalian leather, and the value greatly differs even between the crocodilian species. However, inappropriate labeling of the animal source on leather products sometimes arises from accidental or fraudulent substitution, which is difficult to unambiguously detect by existing methods. In the present study, animal source identification of crocodilian leather was carried out using type I collagen-derived marker peptides generated after dechroming, heat denaturation, and trypsin digestion. Definitive discrimination between the three crocodilian species and also a related species, lizard, was achieved based on the detection patterns of selected six marker peptides, determined by LC-MS. Furthermore, powdering of the leather samples enabled a reduction in the sample amount required and allowed the elimination of the dechroming step. Approximately 100 μg of powder was taken from commercial leather watch straps by filing, resulting in only slight damage to the undersides of the straps. The animal sources of the crocodilian products and also a crocodile-embossed calf product were successfully identified using a combination of the crocodilian marker peptides and previously established mammalian marker peptides. This semi-nondestructive species identification method is not only useful for certification of leather products but also for monitoring of international trade of leather and skin.