Technical Abstract: Three distinctive morphotypes of Zamia occur 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 microsatellite DNA loci 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 allozymes or dominant DNA markers. High infra-populational genetic variation is the rule for all three, perhaps a factor of the high degree of polymorphism in the SSR loci. 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 private alleles; Z. pumila has none. None of the populations appear to have undergone recent bottlenecks, and tests of drift vs. gene flow strongly favor gene flow overall among the populations. Overall, a strong pattern of isolation by distance is evident among Puerto Rican Zamia populations. Zamia amblyphyllidia, Z. pumila and one population of Z. portoricensis are slightly inbred, while two populations of the latter are out-crossing. Significant heterozygote deficiency is evident in Z. pumila and two populations of Z. amblyphyllidia, which may be a cause for concern from a conservation perspective.