On initiative of the government of the Autonomous Province of Bolzano-Südtirol (Province Bolzano-Südtirol, Region Trentino-Alto Adige, Italy) a biodiversity monitoring program was established, starting with sampling on terrestrial sites in 2019 and on running water sites in 2021. The Biodiversity Monitoring South Tyrol (BMS in short) is a long-term project with repetitions on a regular basis. The BMS was launched and is conducted by the Institute for Alpine Environment of Eurac Research in collaboration with the Museum for Nature South Tyrol and the province of South Tyrol’s Nature Conservation Department, as well as the Department for Agriculture. BMS surveys biodiversity throughout the area of South Tyrol and within the most important habitat types, including near-natural, agricultural, and urban habitats. BMS spans sites from the planar zone up to the high alpine zone. At the center of the monitoring are specified monitoring sites; all surveys are conducted in or directly around these sites. In total, we investigate 320 terrestrial survey sites over a period of five years, which is 64 single sites per year. For the monitoring of running waters (in short aquatic BMS) we investigate 120 sites in total over a period of four years.