Biological invasions are one of the major threats to the ecosystem structure and functioning. After the initial introduction, frequently mediated by human activities, alien species can overcome different biogeographical and ecological barriers and determine severe impacts on native biodiversity and socio-economic activities. The Italian peninsula is located at the intersection of large trade routes within the Mediterranean Sea. Such position, along with the intense commercial activity and the high population density of the Italian coast, are considered important drivers of alien species in Italian marine and transitional ecosystems. The Italian peninsula, however, is also one of the regions with the highest native species richness within the Mediterranean Sea and, therefore, it is crucial to account for both alien and native species diversity when estimating the impact of biological invasion. Yet, such comprehensive information is frequently scattered across several biodiversity information systems and databases. Here, two datasets with alien and native species records in Italian marine and transitional waters are described. These datasets, created for the LifeWatch Italy case study on alien species, are the result of a large-scale collaboration involving experts working across the whole range of taxonomic diversity. The marine dataset includes a total of 12,219 records belonging to 3,772 species gathered from 91 investigated sites and seven EUNIS habitats. The dataset on transitional waters biodiversity includes 3,838 records belonging to 2,019 species found in 23 locations and four EUNIS habitats. Alien species were recorded in both marine and transitional waters, accounting respectively for 140 and 171 biological records belonging to 59 and 97 species. These occurrence data can be used for further research studies or management purposes, including the evaluation of the invasion risk and the formulation of alien species control and management plans. Furthermore, these compiled datasets can be used as input data for the Biotope vulnerability case study of LifeWatch ERIC, which offers a number of ICT services for the calculation of the incidence and of the impact of alien species on European biotopes.