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According to recent molecular analyses of Salicornia, we revised the annual glassworts from the Croatian coast, classified until now only as Salicornia europaea. Two species, a diploid Salicornia patula and a tetraploid S. emerici were recognized. They can be easily distinguished by floral characters, but not only by their habitus, which varies extremely according to environmental factors. Both species differ also in seed morphology. Salicornia patula has dimorphic seeds, with larger central seeds reaching high germination rates. Germination patterns helped to explain the habitat preferences. The species rarely co-occur, however. The rare S. patula occupies drier habitats, on coastal mudflats or sands that are irregularly inundated. It occurs within the assoc. Suaedo maritimae-Salicornietum patulae. Salicornia emerici occupies the lowest coastal mudflats, regularly inundated, where nutrient-rich conditions prevail, and forms an almost monotypical assoc. Salicornietum emerici. Due to the synonymy of S. veneta with S. emerici, we exclude the occurrence of S. veneta in Croatia as an independent taxon.