Malvasia nera is one of the minor cultivars belonging to the rich varietal ensemble of Tuscany, one of the most renowned Italian viticultural regions. Starting from data produced in previous researches, it came out that in some cases under the name of ‘Malvasia nera’ it could be grown “Tempranillo”, both in Tuscany and in Basilicata regions. Therefore we started a work to deep inside the identity of these black Malavasias and the results are referred in the present report. In particular, we focused on 16 black Malvasias of Tuscany, keeping 4 registered clones plus accessions grown in different vineyards of the region, some of them being hundred-year-old, in the provinces of Grosseto, Pisa and Arezzo. All the material was analyzed with 11 microsatellite markers (SSR), six of them being those suggested in the frame of the GenRes081 European project. The obtained profiles were compared with data collected in our databases and published in literature, confirming that most of the accessions, including registered clones, share the same molecular profile of Tempranillo. Moreover, ampelographic observations and anthocyanins profiles obtained from chemical analyses on some grapes and wines were compared. From these results it came up that “Tempranillo” is cultivated in Tuscany in historical vineyards with the synonymous “Malvasia nera”.