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Three species of Zamia have been recognized on Puerto Rico: 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. 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 infrapopulational genetic variation 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 private alleles; Z. pumila has none. A strong pattern of isolation by distance is evident among the 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