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Reef coral populations in the western Indian Ocean are neglected in terms of research and management. Very little is known about coral population connectivity and dynamics at regional scales. Platygyra daedalea was collected from Indian Ocean coral reefs, mainly from the east African coast between Mombasa Marine Park (Kenya) in the north and Maputaland (South Africa) in the South. Simple-sequence repeats from five independent loci in the nuclear genome were used to measure differentiation between populations of P. daedalea. Of 350 specimens successfully amplified for one or more simple-sequence repeats, 231 amplified at three or more loci. The remaining specimens comprised a data set including null alleles. Overall heterozygosity was high, He = 0.8, and the mean number of alleles across loci, per population was 4.31. The large numbers of null alleles encountered across loci may be attributed to possible parapatric divergence of the nuclear genome in this genus. Ten populations of the nineteen sampled in this study showed signs of heterozygote excesses and deviation from expectations of Hardy-Weinberg equilibrium. Populations in this study conformed closely to expectations of a panmictic metapopulation with fine-scale structure amongst sub populations (FST = 0.049), although admixture was evident.