The biology of Caiman crocodilus has been studied drawing particular attention to its conservation, due to the commercial uses of the species. However, anatomical aspects such as characteristics of the bony elements of the skull have not been studied in detail in all its geographic range. The characteristics of the skull of the C. crocodilus subspecies were analyzed specifically in Colombian subspecies using geometric morphometrics and descriptive morphology, including geographic and ontogenetic variation. Variations in the shape of the skull were found between the subspecies analyzed by the geometric morphometrics approach, which were also supported by differences at the contact of the frontal and nasal bones, the shape of the ventral suture between premaxilla and maxilla and the palatine process of the maxilla. All populations with trans-Andean distribution in Colombia correspond to C. crocodilus fuscus . Although cis-Andean subspecies present longirostrine skulls, the additional characters support the taxonomic identity of C.c. apaporiensis. Variation in the skull characters in C.c. crocodilus also supports the hypothesis that there are at less two clades on its distribution in Colombia. Then the subspecies differ not only in the shape of the skull, but also in osteological characters, which should be considered in future systematics studies and policies on global conservation.