Foraminifera are an important and useful bioindicator for assessing and understanding marine coastal systems, and their datasets can provide a foundational resource for marine protected area decision-making, identifying polluted or impacted systems, and recognizing patterns of migration and colonization by invasive species. Dominica, a small volcanic island nation located in the Caribbean Sea, is heavily reliant on tourism related to its unique and diverse marine and terrestrial landscapes, flora, and fauna. Monitoring and assessing trends and changes is paramount for the country's economic and environmental health and security; yet, there are still significant knowledge gaps regarding baseline conditions. In response to this, the National Geographic Pristine Seas Project included Dominica in its science-based Marine Protected Areas initiative, which combines scientific research and exploration via surveys and collaborative lobbying efforts, including micropaleontological (foraminifer) study of sediment samples. Foraminiferal assemblages are highly sensitive to habitat type, sediment composition, and food availability, with species composition and abundance often varying significantly between coral reefs, native seagrass meadows, and invasive seagrass habitats; all of which are present in Dominica. Understanding these differences is essential, as they can reveal the ecological impacts of habitat modification and species invasions on benthic communities, as well as provide insight into the resilience and functioning of coastal ecosystems. Despite the ecological importance of foraminifera and their utility in monitoring environmental change, comparative studies on their diversity and distribution across the distinct reef-associated habitats of Dominica remain limited, making the investigation of foraminiferal assemblages across these contrasting habitats critical for establishing baseline data on species richness, composition, and ecological interactions, and for informing conservation and management strategies. The preliminary findings from our study provide insight into the foraminifer community and their associated substrate habitats, both endemic, native, and invasive. For example, worldwide invasive seagrass species Halophila stipulacea and foraminifers such as Amphistegina (various sp.). These findings can support efforts to conserve the island’s diverse marine environments.