Gelidium pusillum is a species reported from the northern Gulf of California to the tropical region of the Mexican Pacific, but there is wide morphological variation among populations. The objective of this research was to evaluate of the Mexican species using morphological and molecular approaches, with the markers rbcL and COI-5P. This study examined 12 samples from four sites in the Mexican tropical Pacific. Phylogenetic analyses resolved these specimens within two clades separated from the topotype material of G. pusillum. The main morphological differences with other Mexican and phylogenetic closely related species were size, branching pattern, branching order, distribution of internal rhizoidal filaments, and shape of the tetrasporangial sori. The sequence divergences between these clades and the morphological differences support their representing distinct species so that Gelidium nayaritense sp. nov. is proposed for tropical specimens of the Mexican Pacific, whose diagnostic characteristics are the little or absent branching, its small size, as well as the presence of internal rhizoidal filaments concentrated in the subcortex, further G. sanyaense is register for first time from Mexico and Eastern Pacific.