Abstract Senecio fontanicola is endemic to black-bog-rush fens of southern Austria, northwestern Slovenia and north-eastern Italy. It is characterized by oblanceolate leaves, a low number of supplementary bracts and glabrous achenes and it grows in marshy spring areas, fens and reed beds, between elevations from 20 to 850 m. The species was never described with molecular traits and during the last decades, S. fontanicola showed a dramatic decline due to land reclamation for agriculture. Therefore, the present study aims to characterize S. fontanicola using the molecular barcoding technique and to updated its distribution to propose a global risk category for the species, based on IUCN criteria. The three molecular markers used in this study (trnH-psbA, rbcL, and ITS) clearly distinguished S. fontanicola from S. doria. s.s. and the revised distribution allowed the definition of the conservation status of the species, that is Endangered-EN B2ab(i, ii, iii, iv) following the B criterion of the IUCN guidelines.