Vaccinium ekmanii Berazain (Ericaceae) is an endemic species from the Dominican Republic whose habitat is particularly vulnerable to human activities due to their proximity to developed areas. Its related species, V. racemosum (Vahl) Wilbur & Lutyen, is native, widely distributed, and is thought to be abundant. Using nine microsatellite loci and pollinator exclusion experiments, this study compared the population genetic structure and the reproductive biology of these two species of Vaccinium in the Dominican Republic to evaluate the impact of anthropogenic activities on their genetic diversity and pollinators. Pollinator exclusion experiments demonstrated that both species are mostly outcrossing, thus they need pollinators to set fruits. Vaccinium ekmanii and V. racemosum have flowers typical of the bee pollination syndrome; the former was confirmed to be bee-pollinated, while the latter was surprisingly pollinated by birds. We found that anthropogenic activities were associated with smaller population size, lower genetic diversity, and low native pollinator frequency. Populations of both species had low-to-moderate levels of genetic diversity and genetic differentiation. The inbreeding coefficients (F_IS) were low in V. ekmanii, and ranged from low to high in V. racemosum. The Bayesian analysis identified two distinct genetic clusters in V. racemosum and three highly admixed groups in V. ekmanii. Our results confirm that habitat degradation had a detrimental effect on pollinators and genetic diversity. Conservation efforts should aim to increase population size and connectivity, and reduce anthropization, particularly in V. ekmanii populations.