Information about a rare allele of phosphoglucomutase (PGM) that is shared by `Braeburn' and 16% of cultivars in the New Zealand Cultivar Collection was combined with historical information about cultivar distribution to select a set of 15 cultivars for a more detailed genetic analysis of their relatedness to the key New Zealand apple (Malus domestica Borkh.) `Braeburn'. DNA from all 16 cultivars was examined by RFLP analysis using 41 probe-enzyme combinations and also by RAPD analysis with 39 selected primers. The RFLP and RAPD data excluded a proposal that `Lady Hamilton' and `Braeburn' are genetically identical. All cultivars except `Lady Hamilton' were excluded as potential parents for `Braeburn' based on incompatible RFLP banding. Assessment of genetic distances between `Braeburn' and the other 15 cultivars from RFLP and RAPD data demonstrated that `Lady Hamilton' was more closely related to `Braeburn' than all others. We conclude that there is a high likelihood that `Lady Hamilton' is one of the parents of `Braeburn'.