The widespread decline of biodiversity due to increasing urban development raises the need to timely identify areas most relevant to the conservation of native species, particularly within cities where natural areas are extremely limited. Here, we assess the multiple role of local geomorphological features in shaping patterns and dynamics of plant diversity, with the aim of identifying conservation values and priorities in an urbanised area of Southern Italy. Based on recent and historical lists of vascular plants, we compared the floristic composition of different portions of the area by considering species’ conservation value, ecological and biogeographical traits. We found that landscape remnants, accounting for 5% of the study area, harbour over 85% of the whole plant diversity and a considerable set of exclusive species. Results of Generalised Linear Mixed Models show an outstanding role of landscape remnants for the conservation of native, rare and specialised species. Based on the compositional similarities among sampled sites resulting from hierarchical clustering, these linear landscape elements also play a key role in maintaining the floristic continuity and potential connectivity throughout the urban landscape. By comparing current biodiversity patterns with data from the early XX century, we also show that the considered landscape elements are significantly more likely to host populations of declining native species, underlining their role as refugia against past and future extinctions. Taken together, our findings represent an effective framework to tackle the challenging conservation of nature in cities, namely providing a valuable approach for the identification of priority areas for the conservation of diversity within anthropogenic landscapes.