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Penicillium expansum and Colletotrichum acutatum cause blue mould and bitter rot of apples during storage which results in significant economic losses. Resistance to these pathogens in commercial apple cultivars has not been documented in the literature. An apple germplasm collection, from the centre of origin in Kazakhstan, is maintained in Geneva, New York. This collection represents a more diverse apple gene pool than commercial cultivars and was evaluated for resistance to the pathogens that cause blue mould and bitter rot. Resistance reactions were skewed towards susceptibility for both fungi and comprised the majority of accessions examined. However, resistance to P. expansum was confirmed in select accessions over multiple years. Maturation patterns and quality indices for soluble solids and acidity, which may also affect susceptibility, were highly variable and represent the genetic diversity of the germplasm collection. Resistance in four accessions to C. acutatum and two accessions resistant to both P. expansum and C. acutatum are reported here for the first time. Data from this study will serve as a foundation for conventional apple breeding programmes and molecular genetics investigations to provide resistance against blue mould and bitter rot in commercial apple varieties.