The Epidaurus UNESCO World Heritage site (EPD) is a famous archaeological area that is located in a small valley in the Peloponnese and receives more than 250,000 visitors annually. The study of the plant diversity of the site is in the framework of a continuous research project concerning archaeological areas of the Peloponnese and in the context of a project by the Ministry of Culture, Education and Religious Affairs of Greece that started during 2023 to study the biodiversity of the archaeological areas of Greece. The main aim of this study is the exploration and analysis of the plant species composition and diversity of the Epidaurus archaeological area, with an emphasis on endemic plants, on ruderal and alien taxa as well as on environmental and disturbance indicators and the cultural ecosystem services they provide. This study revealed a high species richness consisting of 446 plant taxa. Most of them are Mediterranean and widespread, ruderals and medium disturbance indicators, but there are also 12 Greek endemic taxa. The richest in the taxa families are Asteraceae, Fabaceae and Poaceae. Therophytes predominate in the total flora registered and hemicryptophytes predominate in the endemics. Comparisons of the EPD’s plant diversity with other archaeological areas of Greece and the Mediterranean revealed its richness and unique character. Management and protection in archaeological areas such as the Epidaurus must focus on the sustainable conservation of their relationship with their natural environment.