Cyclura ricordii is an endemic iguana from Hispaniola and is listed as Critically Endangered on the IUCN. The main threats are predation by introduced mammals, habitat destruction and hunting. The present study focused on two nesting areas in Pedernales in the Dominican Republic. The hypothesis tested is that natal philopatry influences dispersal and nest site selection. Monitoring and sampling took place during 2012-2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley’s K, revealed that nests were significantly clustered. Hierarchical AMOVA revealed that nest site aggregations did not explain a significant portion of genetic variation. However, Mantel’s tests revealed significant positive correlations between genetic and geographic distance. These results indicate that natal philopatry limits dispersal at a course spatial scale, but does not influence nest site selection at a fine spatial scale.