A wealth of previously unknown pedigree information has been generated for apple (Malus × domestica) through recent studies and an ongoing pedigree identification project using SNP array data. This information has been postulated to be useful in a number of ways for germplasm collections and breeding programs. For example, pedigree information is an important part of genetic characterization of material in germplasm collections. Germplasm collections often seek to preserve cultivars that currently lack commercial relevance but have regional or historical significance or are phenotypically interesting. Pedigree information is often limited on such material. With pedigree information, an accurate genetic structure of these collections can be conveyed to breeders who wish to incorporate novel germplasm into new cultivars. To illustrate ways in which this newly generated pedigree information can be used, we provide examples involving accessions from the germplasm collection Ökowerk and the breeding association “apfel:gut e.V.”, which focus in the development of apples for regional organic production. Both organizations are located in northern Germany. Despite focusing on regional apple cultivars and genetic diversity, many of their accessions and breeding lines are common, cosmopolitan, and foundational cultivars. However, the SNP-based analyses also reveal regionally specific founders, not true-to-type accessions, and genetically unique historical cultivars. This new information has benefitted these organizations by providing genetic characterization that was previously lacking, enabling them to better utilize these genetic resources. Additionally, this information will also be useful in the context of an ongoing larger scale apple pedigree reconstruction project.