Molecular and breeding studies on two pan-tropical marine red algae reveal vastly different levels of genetic variation and reproductive isolation. Sequenced DNA regions from the nuclear, mitochondrial and plastid genomes (partial LSU rRNA, cox2-3 spacer, RuBisCo spacer, respectively) revealed high genetic variation among individuals of Spyridia filamentosa. An rbcL analysis shows that Spyridia is a monophyletic genus distinct from other Ceramiaceae sampled, suggesting that the Ceramiaceae could be paraphyletic. There is complete congruence between all data sets of S. filamentosa, showing a well-supported phylogeographic pattern with samples from the Pacific distinct from Atlantic and Indian Ocean samples. One western Mediterranean sample is associated with Atlantic specimens, while an eastern Mediterranean sample has closer affinities to Pacific samples, possibly indicating a recent cryptic introduction into the eastern Mediterranean. Limited breeding studies imply that these samples are mostly reproductively isolated, whereas a successful cross demonstrated maternal inheritance of organellar DNA. These data indicate that S. filamentosa exists as several cryptic species. Murrayella periclados exhibits low levels of genetic variation and no phylogeographic structure, and almost complete reproductive compatibility between isolates. This suggests that all M. periclados samples share a recent common ancestor that may have dispersed relatively rapidly, or that rates of base pair substitution between these two species vary greatly. Rapid long-distance dispersal of M. periclados is not indicated by what is known of the biology of M. periclados, especially in comparison with S. filamentosa, which appears to be a much better candidate for long-distance dispersal. These data demonstrate that red algal morphospecies are not equivalent units of diversity, with implications for our view of red algal biodiversity and evolution.