Morphological comparisons and molecular phylogenetic analyses were conducted to resolve taxonomic confusion in Cassytha glabella and C. pubescens, both of which were first described from Australia and subsequently considered to be disjunctly distributed between Australia and the Ryukyu Archipelago of Japan. In the morphological comparisons, plants considered as C. pubescens in the Ryukyus differ from C. pubescens in Australia in the presence or absence of hairs on the petals, and those considered as C. glabella in the Ryukyus differ from the C. glabella in Australia in bract and peduncle morphology. The molecular analyses indicated that plants attributed to C. pubescens in the Ryukyus were not closely related to C. pubescens in Australia, and were nested in a clade of populations of a Pan-Western Pacific species C. filiformis. Plants attributed to C. glabella in the Ryukyus were distantly related to C. glabella in Australia. We concluded that plants considered as C. pubescens and C. glabella in the Ryukyus are to be respectively treated as C. filiformis and the Ryukyu endemic species C. pergracilis.