Caulerpa (Chlorophyta, Ulvophyceae) is a common marine tropical-subtropical genus of about 70 species, inhabiting the eulittoral zone on rocks and corals as well as mangroves. The genus is particularly diverse and abundant along southern Australian coasts, where it is thought to have originated. Here, we compare sequences from the nuclear ribosomal cistron among five species of Caulerpa, including nine populations of Caulerpa filiformis from two biogeographic regions: five from Australia and four from South Africa. Species relationships were well resolved by internal transcribed spacer (ITS) sequences and supported by high bootstrap values as follows: (C. geminata (C. simpliciuscula (C. trifaria (C. scalpelliformis (C. filiformis – Australia, C. filiformis – South Africa))))). Nucleotide divergence within C. filiformis was low with four and five nucleotide differences present in ITS1 and ITS2 respectively. Unexpectedly, the 5.8S rRNA gene showed eight nucleotide differences between the Australian and South African populations and may indicate cryptic species. The Australian C. filiformis is probably not a South African introduction. These sequences provide an independent means for assessment of species relationships and appear, in so far as limited taxon sampling permits, to follow chloroplast ultrastructural groupings proposed 20 years ago.