Fire corals are the only branching corals in the South Atlantic and provide an important ecological role as habitat-builders in the region. With three endemic species (Millepora brazilensis, M. nitida and M. taboret and one amphi-Atlantic species (M. alcicornis), fire coral diversity in the Brazilian Province rivals that of the Caribbean Province. Phylogenetic relationships and patterns of population genetic structure and diversity were investigated in all four fire coral species occurring in the Brazilian Province to understand patterns of speciation and biogeography in the genus. A total of 273 colonies from the four species were collected from 17 locations spanning their geographic ranges. Sequences from the 16S ribosomal DNA (rDNA) were used to evaluate phylogenetic relationships. Patterns in genetic diversity and connectivity were inferred by measures of molecular diversity, analyses of molecular variance, pairwise differentiation, and by spatial analyses of molecular variance. Morphometrics of the endemic species M. braziliensis and M. nitida were evaluated by discriminant function analysis; macro-morphological characters were not sufficient to distinguish the two species. Genetic analyses showed that, although they are closely related, each species forms a well-supported Glade. Furthermore, the endemic species characterized a distinct biogeographic barrier: M. braziliensis is restricted to the north of the Sao Francisco River, whereas M. nitida occurs only to the south. Millepora laboreli is restricted to a single location and has low genetic diversity. In contrast, the amphi-Atlantic species M. alcicornis shows high genetic connectivity within the Brazilian Province, and within the Caribbean Province (including Bermuda), despite low levels of gene flow between these populations and across the tropical Atlantic. These patterns reflect the importance of the Amazon Orinoco Plume and the Mid Atlantic Barrier as biogeographic barriers, and suggest that, while M. alcicornis is capable of long-distance dispersal, the three endemics have restricted ranges and more limited dispersal capabilities.