Studying the mating system of wild populations of American crocodiles, Crocodylus acutus, has important conservation implications. We conducted a preliminary analysis of the mating system of C. acutus in Las Baulas (2007 and 2008), Santa Rosa (2007) and Palo Verde (2008 and 2009) National Parks in Guanacaste, Costa Rica. We captured hatchlings during crocodile surveys and analyzed them with nine polymorphic microsatellite loci to determine relatedness values. High relatedness values indicated that full and half siblings were sampled in a single locality and season. We found full siblings between the years that hatchlings were collected in Las Baulas and Palo Verde National Parks, which suggested mate fidelity. The mate fidelity and high relatedness values could be a consequence of the smaller number of adult crocodiles found within these areas or indicative of a small number of dominant males in the populations. Our results support the need to conduct future studies describing the mating system and nesting success within populations of C. acutus. Understanding of these population factors is crucial to the continued success and maintenance of viable populations of C. acutus.