The progress of civilization and the ecological balance on Earth directly depends on the state of biological diversity. Although over 7,000 plant and animal species have been so far identified in the Adriatic Sea, it is important to point out that biodiversity remains insufficiently studied. Recently, there have been changes in the number and composition of the benthic flora of the Adriatic Sea, due to threats like human activities, sea urchin grazing, the emergence of invasive species and climate change. This paper emphasizes the importance of biodiversity, the risks, and categories of endangerment, as well as phytobenthos definition with its features. Selected groups of endangered algae and sea grasses are elaborated in detail, and it is emphasized that even today a detailed mapping of marine flora has not been conducted, independently of level of endangerment, and the data on the species distribution in Adriatic Sea are still incomplete.