To initiate the characterization of the Portuguese grapevine genepool, we have genotyped 49 Portuguese grapevine cultivars at 11 microsatellite loci. The markers proved to be informative in the Portuguese cultivars, with expected heterozygosity ranging from 0.67 to 0.84. At most loci, an excess of heterozygous individuals was observed, while the deficiency of heterozygotes at 1 locus (VVMD6) indicated the presence of null alleles. On the basis of the microsatellite allele data several previously assumed synonyms were verified: (1) 'Fernão Pires'='Maria Gomes', (2) 'Moscatel de Setúbal'='Muscat of Alexandria', (3) 'Boal Cachudo'='Boal da Madeira'='Malvasia Fina', (4) 'Síria'='Crato Branco'= 'Roupeiro' and (5) 'Periquita'='Castelão Francês'='João de Santarém'='Trincadeira'. Although the three varieties 'Verdelho da Madeira', 'Verdelho dos Açores', and 'Verdelho roxo' are regarded by the Lista Nacional de Sinónimos as distinct cultivars, they displayed identical SSR profiles at 17 loci and appear to represent types of 1 single cultivar. The genetic profiles of all 49 cultivars were searched for possible parent-offspring groups. The data obtained revealed the descendence of 'Boal Ratinho' from 'Malvasia Fina' and 'Síria'.