Technical Abstract: Three distinctive cycads are found on Puerto Rico, which have been treated as three species: Z. amblyphyllidia, found on the north coast, and Z. portoricensis and Z. pumila, both found in the south. We investigated the population genetics of these species with ten DNA markers across seven populations, three each of the former two, and one of Z. pumila. Puerto Rican zamias exhibit a combination of the patterns of genetic differentiation that have been reported for cycads based on other types of markers. High genetic variation within populations is the rule for all three. Zamia amblyphyllidia exhibits a more than fivefold greater degree of population differentiation than Z. portoricensis, among whose populations gene flow is much higher. Zamia ambliphyllidia has a greater number of unique alleles; Z. pumila has none. Overall, a strong pattern of isolation by distance is evident among Puerto Rican Zamia populations. Significant inbreeding is evident in Z. pumila and two populations of Z. amblyphyllidia, which may be a cause for concern from a conservation perspective.