Gracilariopsis grevogerungii G.H.Boo & I.K.Hwang, sp. nov., a new species from southern Indonesia, is described based on morphological features and molecular data from two genes: the plastid-encoded rbcL and the mitochondrial COI-5P. Gracilariopsis grevogerungii can be distinguished from other species in the same genus by a combination of traits: terete main axes with irregular branches and scarce short branchlets, and hemispherical cystocarps with up to 3 ostioles and 9–14 cell-layered pericarp. The species occurred on sandy-muddy substrates in the intertidal to the shallow subtidal zone. Phylogenies based on rbcL and COI-5P revealed its sister relationship with the subclade of Gp. heteroclada from China and Gp. mclachlanii from Tanzania. Our results highlight the need for further findings of the agar-yielding Gracilariaceae in southern Indonesia, expanding our knowledge of red algal diversity in tropical Southeast Asia.