Apple (Malus domestica Borkh.) is one of the most widely grown and economically important fruit crops in the world. Skin colour is one of the most important criteria for marketing of apple fruits. Thus, improving fruit colouring is one of the main objectives of apple breeding programs. Even though environmental conditions may affect the colouring of apple, understanding the genetic basis of colouring is important to accelerate the breeding process. In recent years, molecular biology and genetic studies were conducted to explore the molecular basis of colouring in apple. Many genes responsible for the anthocyanin synthesis were identified and their associations with colouring of apple fruit flesh and/or skin were demonstrated. In addition, some DNA markers associated with fruit flesh and skin colour have been developed for screening apple cultivars and hybrids. In this study, 90 apple accessions of international, national, and local decents were selected from the genetic resources collection. Genomic DNA was isolated from leaf tissue of all acession and screened with four different DNA markers associated with fruit flesh and skin colour. Apple accessions in the collection were characterized and their genotypes and genetic potential for fruit colouration were determined by different DNA markers. Additionally, the use of these DNA markers in different apple accessions, well-characterized cultivars and uncharacterized local and national types were investigated.