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Oceanic archipelagos are known to host a variety of endemic plant species. The genetic diversity and structure of these species are important indicators of their evolutionary history and can have consequences on the implementation of appropriate conservation strategies. A comprehensive consideration of the role of their natural history, as well as the landscape features and the geological history of the islands themselves are required to adequately understand the geographic patterns inferred from genetic data. Such is the case for guayabillo (Psidium galapageium), an understudied endemic plant from the Galapagos Islands with important ecological and economic roles. In this study we designed and evaluated 13 informative SSR markers and used them to investigate the genetic diversity, population structure and connectivity of the guayabillo populations from San Cristobal, Isabela and Santa Cruz islands. A total of 208 guayabillo individuals were analyzed, revealing a strong population structure between islands and two distinct genetic lineages for the Santa Cruz population. Overall, the relatively high genetic diversity of the species could be explained by different biological, demographic and environmental factors. For guayabillo populations such as the one in San Cristobal, the history of human disturbance in their habitats might play an important role in explaining their reduced genetic diversity. The coexistence of two distinct lineages in Santa Cruz, with one of them sharing genetic similarities with individuals from San Cristobal, could be attributed to limited, unidirectional gene flow from the latter island to the former. Our findings highlight the complex population dynamics that shape the genetic diversity of species like the guayabillo, and emphasize the importance of a species’ evolution and natural history when interpreting its population genetics.