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Premise of the study: Polymorphic microsatellite primers were developed in the seagrass Halophila ovalis to investigate genetic variation. •
Methods and results: Ten polymorphic microsatellite loci were developed in Halophila ovalis. The number of alleles per locus ranged from 2 to 12 across 80 H. ovalis individuals. These loci were successfully amplified in H. minor, and four were monomorphic across 30 individuals. •
Conclusions: These results from four H. ovalis populations and one H. minor population show the broad utility of microsatellite loci in future studies of population genetics. Four distinct alleles were present in H. minor but absent in H. ovalis, indicating potential divergence between them.