This study focuses on the morphological and genetic characteristics of European crab apple (Malus sylvestris (L.) Mill.) and the occurrence of hybrids in its populations. We analyzed a total of 107 putative European crab apple trees in Slovenia: 92 from nine natural populations, five from a seed stand and 10 from a stand of unnatural origin. We also included 18 domesticated apple trees (Malus × domestica Borkh.) and two Japanese flowering crab apple trees (Malusfloribunda van Houtte) as outliers. The trees were classified into groups of European crab apples, hybrids and domesticated apples according to their morphological and genetic characteristics. Classification based on morphological traits produced different results (58.75% European crab apple, 37.11% hybrids and 4.14% domesticated apple) compared to those based on genetic analysis (70.10% European crab apple, 21.64% hybrids and 8.26% domesticated apple). When genetic and morphological characteristics were combined, only 40.20% of the trees were classified as European crab apple, and an additional group of feral cultivars of domesticated apples (6.18%) was identified. The analysis revealed that hybridization with domesticated apple is taking place in all studied natural European crab apple populations; however, hybrids and feral cultivars only occur to a limited extent. When introducing European crab apple into forests in the future, only genetically verified forest reproductive material obtained exclusively from suitable seed stands should be used.