The reduction of the native forests coverage in mainland Portugal increased in the past centuries, leading to a marked decrease in biodiversity in general, especially on typical species of mature forest environments. However, urban biodiversity seems to resist more effectively than rural to disturbances due to the lower incidence of fires, as well as to agriculture expansion. Thus, in this work, we analyzed the dynamics of the natural vegetation potential in each biogeographic sector, and selected, based on the evolutionary stages of the vegetation, a set of priority taxa for conservation. The criteria used are intended to highlight plants with ornamental value, but at the same time, some of them have high patrimonial value, belonging to the Red List of Vascular Flora of Mainland Portugal or protected by Annexes II, IV and V of the Sectorial Plan of the Natura 2000 Network at the European level. Our analysis resulted in the identification of 62 plants that can be increased in public spaces in order to improve their conservation status. For each biogeographic sector, the plants best adapted to the local edaphoclimatic conditions are presented. Forest habitats can now, through micro-reserves in urban areas, ensure their long-term conservation and greater awareness among the population. An integrated planning, where the socio-ecological strategy is designed for the long term, will benefit the quality of life of citizens in an urban environment. Furthermore, the creation of micro-reserves in urban parks (gardens) can prevent the extinction of many botanical values in the landscapes of the western Mediterranean Basin.