Research Highlights: Pestalotiopsis pini sp. nov. is an emerging pathogen on stone pine, Pinus pinea L., in Portugal. Background and Objectives: Stone pine is one of the most important forest tree species in Portugal and in the whole Mediterranean basin. Pestalotiopsis species are common endophytes, saprobes or pathogens in a variety of hosts and environments. The objective of the present study was to identify the Pestalotiopsis species associated with the symptomatic stone pine trees. Materials and Methods: Samples of stone pine trees showing shoot blight and stem necrosis were obtained from stone pine orchards and urban areas in Portugal, and the isolated Pestalotiopsis species were identified based on morphology and combined ITS, TEF and TUB DNA sequence data. Artificial inoculations on one-year-old stone pine seedlings were performed with the two species most frequently found in association with shoot blight disease. Results: Five Pestalotiopsis spp. were isolated. A taxonomic novelty, Pestalotiopsis pini is described, representing a new pathogen for stone pine. Conclusions: Pestalotiopsis species may represent a threat to the health of pine forests in the Mediterranean basin. Future research should be done in order to increase our knowledge about the potential impact of pestalotioid species in stone pine, in order to develop management strategies against these pathogens.