Unmanned aerial vehicles (UAVs), commonly known as drones, present a cost-effective solution for the swift collection of data from vast and remote areas that are otherwise difficult to access. The Mediterranean Basin, known for being a hot spot for plant biodiversity, hosts several habitats and taxa of significant naturalistic value. However, many of these areas are often inaccessible to botanists, making exploration and research challenging. The aim of this paper is to involve the utilization of drone surveys and open-source software for botanical research. Our primary goal is to show the effectiveness of these tools in the field and demonstrate their practical application in Natura 2000 sites. The protected area chosen for this research is Rocca di Novara, situated in northeastern Sicily. Thanks to our drone investigations, we were able to capture images of the mountain’s side that is inaccessible to humans. This allowed us to observe the habitat of some species in detail. One of the most fascinating discoveries was the reappearance of Saxifraga callosa subsp. australis, which had not been confirmed in this area for over 140 years. Using drones for botanical research can boost field research, making monitoring easier and more cost-effective over time, especially in Natura 2000 sites.