Background <p><i>Atrina vexillum</i> (Born, 1778) is a bivalve mollusk indigenous to the Indo-Pacific coastal regions. Despite being a species of high ecological and economic value, it remains largely understudied and estimates of population genetic diversity and structure are urgently needed. Microsatellite markers are useful for assessing population genetic structure due to their high polymorphism. This study aimed to develop 30 novel, highly polymorphic, microsatellite markers for <i>A. vexillum</i>.</p> Methods and results <p>A total of 30 markers were optimized for reliable amplification. They were tested by multiplex PCR in 92 individuals sampled in Bora-Bora and Raiatea islands (French Polynesia). The number of alleles per polymorphic locus (<i>n</i> = 29/30) ranged from 3 to 18. Null alleles were suspected for 6 of the markers. The F_IS values per locus calculated over all sampled individuals ranged from − 0.0174 to 0.870 (mean 0.107) and were significant for 7 loci. The observed heterozygosity per locus ranged from 0.168 to 0.920 (mean 0.66), values significantly higher than those obtained with markers previously developed for the species. Cross-species amplification has not been successful in <i>Pinna nobilis</i> individuals.</p> Conclusion <p>These 30 microsatellite markers demonstrate high polymorphism and will be key in assessing the genetic diversity and structure of <i>A. vexillum</i> populations in French Polynesia. They are a step towards analyzing parentage and further understanding the population dynamics and establishing effective conservation measures for a species that is declining without clearly identified causes.</p>