Seagrasses are the structural species of one of the most important coastal ecosystems worldwide and support high levels of biodiversity and biomass production. Posidonia is one of the most ancient seagrass genera and displays a contrasting disjunct biogeographic pattern. It contains one single species in the Northern Hemisphere, P. oceanica, which is endemic to the Mediterranean Sea, and has up to 8 recognized taxa in the Southern Hemisphere, which in Australia are divided into 2 complexes, P. ostenfeldii and P. australis. A phylogeny based on a nuclear marker (rRNA-ITS) revealed an ancient split between the northern (i.e. Mediterranean) and southern (i.e. Australian) taxa, followed by a separation of the 2 recognized Australian complexes. However, the species belonging to the P. ostenfeldii complex were indistinguishable, suggesting an ecotypic origin or a recent speciation. Therefore, among the 7 morphologically described Australian species only 4 species lineages can be discriminated. The organelle markers nad7 intron, trnL-F and matK/trnK intron were not informative for reconstructing the phylogeny of this genus, and the mitochondrial markers exhibited a strikingly slow evolutionary rate relative to other genome regions.