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Morphological data has provided a basis for the hypothesis that three taxa belonging to the Caulerpa racemosa complex occur in the Mediterranean Sea: var. turbinata–uvifera, var. lamourouxi, and the ‘invasive variety’. In order to test this hypothesis and to determine the origin of the ‘invasive variety’, the transcribed spacer ITS1–ITS2 and an 18S ribosomal DNA (rDNA) intron were analysed from 16 isolates of Caulerpa racemosa. The ‘invasive variety’ shows intraindividual polymorphism for both types of sequences. The ITS1–ITS2 data confirm that the three morphological varieties of C. racemosa from the Mediterranean Sea are distinct taxonomic units. The 18S intron data suggest that the new ‘invasive variety’ could be a recent hybrid between var. turbinata–uvifera and an unknown tropical strain. Incongruence between the phylogenetic tree computed from ITS1–ITS2 regions and the 18S intron indicates that homogenization processes of concerted evolution have run at different rates.