The vegetation of the European Natura 2000 protected area of Spercheios river and Maliakos gulf, that includes Mediterranean sclerophyllous shrublands, as well as riverine and coastal habitats, was studied during 2000 and 2014–2015. The vegetation was analysed following the Braun-Blanquet method. Twenty six plant communities were recorded, one of which (Pistacio terebinthi-Quercetum cocciferae) described for the first time. The communities belong to fifteen alliances, fourteen orders and eleven phytosociological classes. The distinguished vegetation units are described, presented in phytosociological tables and compared with similar communities from other Mediterranean countries. Eleven different habitat types were identified. Two of them (“Quercus coccifera woods” and “Reed beds”) are Greek habitat types, while the rest are included in Annex I of the Directive 92/43/EEC. Three of the latter (1420, 2110, 3170) have a scattered presence in the Natura 2000 network in Greece, while one (3170) is a priority habitat type.