ABSTRACT Anadara tuberculosa is a bivalve mollusk common in the mangroves of the Panamanian Pacific, subject to commercial exploitation throughout its distribution area. Fishing pressure, combined with environmental contamination processes, is a factor that can influence the genetic structure of the species. Understanding the genetic aspects of A. tuberculosa is relevant for developing conservation policies; therefore, this study analyzed the genetic diversity, structure, and demographic history of this species in five localities of the Panamanian Pacific using the mitochondrial COI gene. The results revealed high haplotypic (0.93–0.97) and low nucleotide (0.0076–0.0095) diversity with generally low genetic differentiation, although significant structure was detected specifically between Coiba and Isla Cañas. Demographic analyses and a star‐shaped haplotype network indicate a recent population expansion, a signal that was most pronounced in the Chame locality. The low genetic differentiation is attributed to the presence of coastal currents and geographical barriers, which together shape each site and influence larval dispersal and cause some degree of genetic connectivity. This study provides a preliminary genetic baseline that can support the design of site‐specific management actions and periodic genetic monitoring aimed at preserving diversity and contributing to the long‐term sustainability of this essential resource for harvesting communities and the ecological processes occurring in the mangrove ecosystems of the studied localities.