Headstarting is one of the more recent practices being used to maintain endangered populations in the wild. A headstart program was developed for the Jamaican iguana, Cyclura collei, in 1991 after its rediscovery in 1990. This current study tests the hypothesis that this population is experiencing a reduction in effective population size in spite of an increasing census population size due to the small number of nests available in the early years of the headstart program. A total of 875 individuals collected from 1991 to 2011 were genotyped at twelve variable microsatellite loci. Results from this study indicate a slight but significant decline in genetic variation (3% loss), and a modest proportional reduction in effective population size (0.075), since the initiation of the program. However, it is important to note these data also suggests that effective population size of this population is stabilizing.