The lack of information surrounding natural history and ecology of the endangered Morelet's crocodile (Crocodylus moreletii) has prompted a baseline study of the population genetics for this species. Nine microsatellite loci have been used to estimate genetic structure within and gene flow patterns among crocodiles (using a recently described maximum likelihood approach) from seven localities in north-central Belize. Individuals from the seven localities grouped into four apparent populations. Within localities, a high degree of genetic heterogeneity was observed. Among all localities, some subdivision was present (F_ST = 0.062; R_ST = 0.100). Furthermore, among the apparent populations, we found a significant correlation between geographic distance and genetic subdivision. Our findings suggest a relatively high level of migration among populations (Nm = 5.15) and are consistent with an isolation-by-distance model of gene flow. Two contiguous subpopulations in particular, New River and New River Lagoon, may form an important source for genetic variation for smaller populations throughout the region. These data will allow us to test hypotheses of relatedness among C. moreletii for other drainages in Belize and will be useful in optimizing future management programs for C. moreletii.