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Recent molecular phylogenetic studies reported high diversity of Ruppia species in the Mediterranean. Multiple taxa, including apparent endemics, are known from that region, however, they have thus far not been exposed to phylogenetic analyses aimed at studying their relationships to taxa from other parts of the world. Here we present a comprehensive phylogenetic analyses of the R. maritima complex using data sets composed of DNA sequences of the plastid genome, the multi-copy nuclear ITS region, and the low-copy nuclear phyB gene with a primary focus on the Mediterranean representatives of the complex. As a result, a new lineage, 'Drepanensis', was identified as the seventh entity of the complex. This lineage is endemic to the Mediterranean. The accessions included in the former 'Tetraploid' entity were reclassified into two entities: an Asia-Australia-Europe disjunct 'Tetraploid_α' with a paternal 'Diploid' origin, and a European 'Tetraploid_γ' originating from a maternal 'Drepanensis' lineage. Another entity, 'Tetraploid_β', is likely to have been originated as a result of chloroplast capture through backcrossing hybridization between paternal 'Tetraploid_α' and maternal 'Tetraploid_γ'. Additional discovery of multiple tetraploidizations as well as hybridization and chloroplast capture at the tetraploid level indicated that hybridization has been a significant factor in the diversification of Ruppia. [ABSTRACT FROM AUTHOR]