Bitter pit is one of the most economically-important physiological disorders affecting apple fruit production, causing soft discrete pitting of the cortical flesh of the apple fruits, which renders them unmarketable. The disorder is heritable, however the environment and cultural practices play a major role in expression of symptoms. Bitter pit has been shown to be controllable to a certain extent using calcium sprays and dips, however, their use does not entirely prevent the incidence of the disorder.Previously, bitter pit has been shown to be controlled by two dominant genes, and markers on linkage group 16 of the apple genome were identified that were significantly associated with the expression of bitter pit symptoms in a genome wide association study. In this investigation, we identified a major QTL for bitter pit defined by two microsatellite (SSR) markers. The association of the SSRs with the bitter pit locus, and their ability to predict severe symptom expression, was confirmed through screening of individuals with stable phenotypic expression from an additional mapping progeny. The data generated in this current study suggest a two gene model could account for the control of bitter pit symptom expression, however, only one of the loci was detectable, most likely due to dominance of alleles carried by both parents of the mapping progeny used. The SSR markers identified are costeffective, robust and multi-allelic and thus should prove useful for the identification of seedlings with resistance to bitter pit using marker assisted selection in apple breeding programs.