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This study builds on recent treatments of the marine red algal family Gracilariaceae (Gracilariales) focusing in detail on Hydropuntia and Crassiphycus. Species in these two genera often present identification problems due to high levels of morphologial similarity among genetically distinct species, and high levels of phenotypic plasticity, leading to pseudocryptic speciation and homoplasies. In order to resolve long standing problems, clarify some species concepts and better understand the evolution of the group, we performed phylogenetic analyses of all plastid rbcL DNA sequences available for known Hydropuntia and Crassiphycus species, including newly sequenced specimens. Our results revealed the presence of potentially undescribed species, the existence of strong phylogeographic patterns below and above the species level and helped re-delineate morphologically similar taxa. New detailed morphological descriptions for three common yet poorly known Western Atlantic species are provided: C. secundus, C. usneoides and H. rangiferina. H. rangiferina from the Indo- Pacific is a distinct species from the true H. rangiferina and represents a putative undescribed species. We also provide a time-calibrated phylogeny for the six genera in the Gracilariales to identify past geological and climatic processes associated with their origin and diversification.