Astragalus vesicarius subsp. pastellianus is present in the most xerothermic parts of the Italian Alps at a few localized sites. Two populations are known from the Adige region, one at the locus classicus at Monte Pastello (lower Adige, Lessin Mountains) and another in the Vinschgau Valley (upper Adige), and there is a further population 250 km westwards in the Aosta Valley. The relationships of this taxon were investigated with molecular sequencing and fingerprinting methods. Astragalus vesicarius subsp. pastellianus shows a clear genetic differentiation in a Western and an Eastern lineage as it is known from several other alpine and subalpine species. The population at Monte Pastello is closely related to the populations in the Aosta Valley and to the subspecies vesicariusfrom the French Alps, whereas the populations from the Vinschgau Valley (South Tyrol) belong to the Eastern lineage, together with the subspecies carniolicus from the Julian Alps. Therefore, the origin of the Vinschgau populations seems to be in Eastern refugia and not in the open Southern Adige Valley which would be plausible from a geographical point of view.