Comparative sequence data from the rDNA ITS have proven very useful in species identification and identifying major biogeographic groups of Caulerpa taxifolia. However, the low variability of the sequence, and the need to screen hundreds of samples has limited its utility for population level studies. Here we report on the performance of two new markers suitable for population level screening: the chloroplast rDNA 16S intron-2 and inter-simple-sequence-repeat fingerprints (ISSRs). A new analysis of ITS1 insertion-deletion patterns was also conducted using all available sequences. A number of new insights have emerged. First, the invasive aquarium strain (Mediterranean, California) is clearly from Brisbane, but the Brisbane populations themselves may be the result of an introduction from Northern Australia. Second, an analyses of the new data in conjunction with an ITS1-insertion-deletion analysis further suggests that the Mediterranean populations may be the result of not one, but two separate introductions. Third, intra-population genetic diversity between invasive Mediterranean and "native" Australian populations revealed the occurrence of two divergent and widespread clades. The first clade grouped non-tropical invasive populations with coastal inshore populations of Australia while the second clustered all offshore/oceanic populations so far studied. Caulerpa taxifolia, therefore, exists as a complex of independent ecotypes that probably represent nascent species. Fourth, despite our finding of nine distinct nuclear and five distinct chloroplast profiles, strong linkage disequilibrium was found in most specimens, which indicates a predominance of asexual reproduction. However, nucleo-cytoplasmic recombination was detected in one case, supporting hybridization both within and between populations.

Key words: Caulerpa taxifolia, Chlorophyta, invasions, molecular markers