Since the first recorded Tropical Western Atlantic sightings of the Indo-Pacific Lionfish (P. volitans and P. miles) in the 1990s, this mid-level predator has become a common component of shallow-water fish assemblages from mangrove creeks to coral reefs. Although the origins of this cryptic invasion are unknown, the success of lionfish, specifically in the near shore waters of The Bahamas, has been document through increased abundance and increase in the number of benthic habitats utilized since 2005. The long term impact of lionfish on near shore fish assemblages in the wider Caribbean is not known, but invasive species management planning requires some information on changes in the abundance and diversity of reef fishes, especially species commercially exploited. This large synoptic survey of fish assemblages from four types of reef habitats on two islands in The Bahamas examines how the presence of lionfish can alter shallow-water tropical fish assemblages. Patch reefs, hard bottom, fringing reefs and channels reefs adjacent to the islands of Great Exuma (Central Bahamas) and Great Inagua (Southern Bahamas) were evaluated via a rapid assessment methodology. Roving diver fish surveys were carried out with a coastal assessment of anthropogenic impacts (ranking) from development and/or fishing pressure. Univariate and Multivariate statistics were used to determine if the presence of lionfish is significantly altering the recorded fish assemblages when compared to sites with no lionfish present. This community-level assessment can be applied in the understanding of how the lionfish invasion may affect near shore reef habitats, and ultimately the production of commercially important fisheries species.