The systematics and the phylogenetic position of the Caribbean representatives of Phaenonotum Sharp (Coleoptera: Hydrophilidae) are investigated in order to understand the composition of the Caribbean fauna and its origin. Phylogenetic analysis based on mitochondrial and nuclear genes has revealed the Caribbean species to be situated in three deeply nested clades, inferring multiple colonization of Caribbean islands from the continent. Time-tree analysis and BioGeoBEARS analyses of ancestral ranges estimated the oldest clade, consisting of wingless single-island endemics of Cuba (P. delgadoi), Jamaica (P. ondreji sp. nov.) and Hispaniola (P. laterale sp. nov.), to have diverged ca. 46.6 Ma from the South American ancestor and subsequently colonizing the Caribbean most likely via the GAARlandia land bridge connecting South America with Greater Antilles. The remaining three Caribbean species, including the Puerto Rican endemic, P. borinquenum sp. nov., are of more recent (Miocene to Pliocene) origin and colonized the Greater Antilles by over-water dispersal. All the Caribbean species are illustrated and diagnosed and three new species are described. The genus Phaenonotum, excluding P. caribense Archangelsky, is confirmed as a monophylum. We demonstrate that species-level taxonomy of Phaenonotum is difficult to solve by morphology alone, and ideally requires the combination of morphology and molecular markers.