Long-term investigation of charophytes in the West and Central Balkans has confirmed an exceptional level of diversity of these macroalgae in the region. Charophytes have been observed in the fresh, brackish, salt and mineral waters of different aquatic environments from the Adriatic coast up to alpine zones. Forty two species of all extant genera of charophytes were identified, including 25 species the genus Chara, 10 species of Nitella and 4 of Tolypella. Only one species of the genera Lychnothamnus, Lampro-thamnium and Nitellopsis has been found. Aquatic environments in the coastal Adriatic zone, such as the lakes of the Krka River, the estuary of the Neretva River in Croatia and Lake Skadar in Montenegro, are notable for the great abundance of various charophytes. This is no less true for the glacial lakes on Mts Zelengora and Durmitor in Montenegro and the deep and ancient lake of Ohrid in FYR Macedonia. All these habitats are centers of charophyte diversity and, as such, deserve particular attention and protection.