The small Indian mongoose has been introduced into several important hotspots of biodiversity and is considered the wild carnivore with the greatest negative impact on autochthonous ecosystems. Understanding the introduction and dispersal history of the species is crucial in any effort to conserve global biodiversity. We investigated the genetic structure and diversity of the small Indian mongoose, with a focus on the Caribbean region, using genetic data from 496 individuals. We performed molecular genetic analyses using two mitochondrial and eleven newly designed microsatellite markers. We compared our results with historical records and scenarios inferred from the literature. Consistent with historical records, molecular results suggest multiple introduction events into Jamaica from India, as well as the subsequent introduction of the species from Jamaica into Grenada and Puerto Rico. Our results also suggest new scenarios for other introduced populations. For instance, the introduction history of the species into Guadeloupe may be more complex than previously thought, sharing a common origin with the populations of Jamaica, Trinidad and Guyana. In addition, microsatellite data reveal a strong structuration of the populations within the West Indian islands, including nearby islands within the Guadeloupean archipelago, highlighting the lack of dispersal events between islands after the initial introductions. Conversely, the absence of structure inside each island indicates the high dispersal ability of the small Indian mongoose within these islands. These results and the newly developed microsatellite markers represent valuable tools to identify the origin of potential new introductions.