Ruppia cf. maritima is one of the few native Hawaiian brackish water flowering plants, but its identity has never been examined using genetic analysis. The ability of this seagrass to tolerate a wide range of salinities and temperatures is reflected in its morphological variability among locations worldwide. Three populations on the island of Hawai‘i were sampled, and molecular analyses of the nuclear gene ITS and two chloroplast genes trnH-psbA and rbcL were used to examine the identity of Hawaiian Ruppia. Concatenated analyses showed that the populations contained little intra- or interpopulation variability, and indicated greatest genetic similarity to specimens from Japan, India, Vietnam, and Africa. Slight variations in tree topologies were present among the individual nuclear and two plastid markers; however, all Hawaiian specimens nested within other sequences reported as R. maritima. Molecular phylogenetic analyses demonstrate that there are multiple clades of samples from around the world labeled as R. maritima, and that the Hawaiian samples are allied with one of these clades. The geographic isolation and geologic age of each Hawaiian island, as well as the disjunct distribution of Ruppia populations among islands and within each island suggest a multiplex biogeography and evolutionary history of Hawaiian Ruppia.