The small giant clam, Tridacna maxima, is distributed from the Red Sea and East African coast to French Polynesia. Across this widespread Indo‐Pacific range, T. maxima shows strong population structure, in agreement with its limited dispersal abilities. Peripheral populations may have smaller effective population sizes, increasing their vulnerability under any environmental changes. Understanding evolutionary processes at play in such regions located at the edges of T. maxima distribution is a prerequisite in the context of transfers and restocking programmes. In this study, giant clams were sampled from 14 atolls and islands within four archipelagos in the peripheral region of French Polynesia, in 2001–2002 and/or in 2012–2013, then genotyped at the COI gene and at nine microsatellite loci. Mitochondrial lineages of T. maxima from French Polynesia diverged from those sampled in Micronesia, Melanesia, the Coral Triangle and the Red Sea by 6.6–7.3%. Within French Polynesia, significant genetic structure was found, indicating restricted gene flow, and it was stable through time. Most of the genetic variation at microsatellite loci was between archipelagos. The most differentiated archipelago was the most geographically isolated (the Austral Islands). The current patterns of genetic structuring of T. maxima in French Polynesia probably result from long‐term genetic isolation with limited dispersal ability. In addition, these results underlined that sufficiently large populations of T. maxima have persisted in the Central Pacific during the last sea‐level regression. Strategies to optimize transfers and restocking programmes should be designed to preserve the genetic diversity and structure observed here, to avoid the risks of altering the genetic structure, allele loss and/or introduction of maladapted alleles in the receiving populations.