Molecular techniques have proven useful not only in resolving taxonomic and systematic issues among several genera in the red algal family Gracilariaceae but also in the rapid identification of cryptic invasive species (e.g., Gracilaria vermiculophylla and G. parvispora). In Hawai‘i (U.S.A.), Gracilaria is both economically and culturally important, with G. coronopifolia being highly prized. Molecular analyses of chloroplast rbcL and mitochondrial COI sequence data indicate that recent collections of Hawaiian “ G. coronopifolia” are polyphyletic and consist of two species representing two different genera, Gracilaria and Hydropuntia. This is the first formal record of the genus Hydropuntia in Hawai‘i. These results also reveal that collections of Hawaiian Hydropuntia sp. are closely related to an Australian alga, Gracilaria perplexa, with both taxa belonging to a strongly supported Hydropuntia clade, and suggest that both cases represent cryptic invasions. We formally propose the transfer of G. perplexa to Hydropuntia and also recognize Hawaiian specimens of Hydropuntia as that species: Hydropuntia perplexa (Byrne & Zuccarello) Conklin, O'Doherty & A. R. Sherwood, n. comb.