Old grapevine (Vitis vinifera L.) accessions are a source of genes that could be rescued for use per se or in modern breeding programs. The first step in this rescuing is collecting and characterizing the germplasm from a particular region. This study presents the genetic characterization of 21 grapevine accessions collected from the Atacama Desert in the far North of Chile. Characterization was based on 12 microsatellites (Simple Sequence Repeats, or SSRs) supplemented with Amplified Fragment Length Polymorphic (AFLP) markers. Most of the collected accessions produced red berries and shared the genetic characteristics of the cv. País, an old genotype found throughout America. However, among those red-berried accessions, one showed a severe abortive phenotype (22S7), and another (6S4) differed from ’País’ in one allele. Both could be examples of somatic mutations, even though no variations in their AFLP patterns were found. On the other hand, the only accession with red berries that exhibited genetic characteristics different from those of ’País’ (5CN) corresponded to ’Gros Colman’, a supposedly Georgian genotype introduced to this region by the mid-20th century. Greater genetic diversity was detected among the white and pink accessions, which were classified into five clades based on their SSR allelic patterns. Of these genotypes, 11Si was identified as ’Emperatriz’ or ’Red Seedless’, an Argentinean variety; accessions 16H1 and 17H2 corresponded to a product of crossing ’País’ and ’Muscat of Alexandria’; and, finally, accession 20S5 was identified as ’Ahmeur bou Ahmeur’, an Algerian genotype harboring pink berries. Two seeded genotypes harboring small and large white berries were not identified as known varieties. The possible use of these accessions for breeding to enhance survival in the harsh environment of the Atacama Desert is discussed.