Conservation efforts have allowed American crocodile (Crocodylus acutus) populations to recover to the point that dispersal movements are beginning to be documented. The environmental authority of San Andres Island in Colombia reported, for the first time, the arrival of two C. acutus from unknown localities in 2012 and 2018. The former was sacrificed, and the latter was captured and kept in captivity to determining its potential origin. We used wildlife forensics to establish the origin of the animal that arrived in 2018 based on two mitochondrial genes (COI and Cytb). Additionally, five other samples from Tayrona National Natural Park (TNNP), and Salamanca Island Road Park (SIRP) were sequenced for molecular attribution of these populations to the currently described lineages. Phylogenetic and phylogeographic analyses showed that the American crocodile found in San Andrés belongs to a continental evolutionary lineage endemic to Colombia, showing also a strong genetic similarity with animals from SIRP. Thus, the most likely origin for this individual was not the nearest continental area but somewhere around the central Colombian Caribbean, located ~700 km from the island. We discuss the implication of our findings in the systematics and conservation of the species and the potential of mitochondrial DNA analysis to identify such migrants.