The section Opuntia within the green seaweed genus Halimeda includes sprawling and pendant thalli composed of strongly calcified segments. Within this section, identification of Atlantic material is straightforward, but Indo-Pacific material is often difficult to key out. This is particularly true for specimens resembling H. opuntia, H. distorta, and H. hederacea; many specimens do not fit any type or are morphologically intermediate. The goals of the present study are to define morphologically and genetically distinct groups among such specimens and to assess phylogeographic patterns within these groups. Specimens were collected throughout the geographical and morphological range. Sequences of H. minima and H. gracilis were included as outgroups. Two morphological groups were discerned within the ingroup; the first fit H. opuntia, whereas most specimens in the second group, referred to as the distorta–hederacea complex, did not fit any species description unambiguously. The latter were subdivided into two subgroups corresponding more or less to H. hederacea and H. distorta, yet intermediates between these morphs existed. A phylogeny inferred from partial nuclear rDNA sequences showed one lineage with H. opuntia and a second one containing the distorta–hederacea complex, thus corroborating the two major morphological groups. The distorta–hederacea complex contained two clades that show only partial correspondence with the morphological subgroups. Therefore, H. hederacea is synonymized with H. distorta. Phylogeographic structure within H. opuntia indicated that this species dispersed from the Indo-Pacific into the Atlantic. Fossil records of the species also show occurrence at Pacific sites throughout the last 105 years and a sudden appearance in the Caribbean and Bahamas during the last millennium.