The identification of a crocodile is a complex process. The most used method is invasive and dangerous. Recently, a new method, non-invasive, was introduced, in which the crocodile is identified by its number of post-occipital scales, nuchals, and backs. However, the scale count is done manually. In this work, we present a method based on image processing for the identification and counting of scales improving the above-mentioned method. The results obtained are reproducible and more reliable, facilitating the identification of the crocodiles for their population study.