Haplotype analysis is a powerful technique for tracking identical-by-descent segments in breeding populations. Over the last several years we have created over 100 F1 diploid populations, derived from a limited set of S. tuberosum dihaploid founders that includes US-W4, a known carrier of the Sli haplotype for self-compatibility. Of the more than 1000 F1 individuals that have been either selfed or sib-mated, a small number produced F2 populations that were evaluated in greenhouse experiments for vine maturity, pollen and true seed production, and tuber traits. The objective of this research was to reconstruct F2 individuals in terms of the founder haplotypes and select parents based on the combined genetic and phenotypic data. F2 individuals and their parents were genotyped using the potato SNP array. Marker data were used to check the recorded pedigree and infer founder haplotype probabilities using the polyBreedR and RABBIT software packages, respectively. Three F2 progeny (W2x001-22-45, W2x082-14-13, and W2x082-14-24) with good pollen shed and self-fertility were determined to be homozygous for a haplotype derived from US-W4 at the published location of Sli on chromosome 12. These individuals also displayed early vine maturity and were homozygous for a haplotype derived from US-W4 at the location of the CDF1 gene on chromosome 5. Based on these characteristics and their desirable tuber traits in the greenhouse experiments, the F2 progeny have been used as parents for future breeding cycles.