Algae from the Caulerpa genus host internal dense microbial communities thought to play an important role in development, defense and metabolic activities of the algae. Here we assess and compare the diversity of the endophytic bacterial community of the three species co-occurring in the Mediterranean, two invasive and one native. Endophytic bacterial communities of Caulerpa taxifolia (invasive) C. racemosa (invasive, two distinguished varieties) and C. prolifera (native) from four Mediterranean localities were characterized through 16S rRNA tag-Pyrosequencing. Multivariate analyses and data plots showed that bacterial communities cluster according to host species rather than habitat. However one-Way ANOSIM also revealed some similarity among communities from geographically neighboring areas. Most common classes were ? and ß Proteobacteria and three different bacterial sections were identified among SUs. The persistent core community shared among all species and locations was dominated by the groups Burkholderiales and Pseudomonadales. Species-specific OTUs in these communities were dominated by the Orders Kiloniellales in C. prolifera and Oceanospirillales in C. taxifolia, whereas no conspicuous group was found to be most prevalent in any of the two C. racemosa varieties. The variable section is most probably the dynamic bacterial portion that is environmentally acquired. Indirect evidence based on Blast suggest that these bacterial communities may play an important role in the metabolism of their algal host, in particular on their ability to grow on highly anoxic sediment. These results call further functional genomic analysis in order to test for this possible role as if c onfirmed bacterial communities may contribute actively to the competitiveness of their host algae, in particularly in community they have been recently introduced in.