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Sodium (Na+) exclusion is an important rootstock trait, which contributes to the overall salt tolerance of a grafted vine by limiting Na+ accumulation in both leaves and berries. A population of 68 hybrid Vitis genotypes, presumed to be from a cross between the rootstocks ‘K51-40’ and ‘140 Ruggeri’, have previously been investigated for their ability to exclude Na+. Here we report that the genotyping of this population with eight short sequence repeat (SSR) markers showed that ‘140 Ruggeri’ is the male parent of only 40 individuals. The rootstock ‘Schwarzmann’ is the male parent of 18 genotypes, with the remaining 10 genotypes being derived from unknown pollen sources. The role of HKT1;1 in Na+ exclusion in the 40 ‘K51-40’ × ‘140 Ruggeri’ hybrids has previously been reported, with four unique alleles of this gene present in this family, with each parent heterozygous for a dominant allele (EK or ER) linked with strong exclusion and for a recessive allele (eK or eR) linked with poor exclusion. In the present study, we found ‘Schwarzmann’ is also heterozygous for HKT1;1 alleles, consisting of dominant (EK) and recessive (eK) alleles identical to those of ‘K51-40’. The 18 ‘K51-40’ × ‘Schwarzmann’ hybrids were scored for inheritance of these alleles. When screened for the Na+ exclusion phenotype, two homozygous eKeK genotypes accumulated less Na+ than eKeR hybrids having ‘140 Ruggeri’ as the pollen parent. Thus, it appears that the recessive eR allele from ‘140 Ruggeri’ results in higher Na+ accumulation than the recessive eK allele from ‘K51-40’ or ‘Schwarzmann’, and this is supported by functional Na+ transport rates of the encoded HKT1;1 proteins previously reported.