Traditionally, sweet cherry (Prunus avium L.) cultivars are propagated on seedling rootstocks in Turkey. For this purpose, wild cherries (P. avium) and 'Mahaleb' (P. mahaleb L.) have been used extensively. The use of clonal (vegetatively propagated) rootstocks for sweet cherries is low in Turkey due to the high cost of nursery plants. Seeds for rootstock propagation usually are collected by nurserymen from trees of unknown origin. The objectives of this study were to compare the seedlings of two Prunus species for morphological characteristics and to detect any isozyme polymorphisms in seedling populations. During the study, variations in germination rate, leaf area and seedling size were evaluated. Isozyme variation was surveyed for five enzymes including alcohol dehydrogenase (ADH, EC 1.1.1), isocitrate dehydrogenase (IDH, EC 220.127.116.11), malate dehydrogenase (MDH, EC 18.104.22.168), peroxidase (PRX, EC 22.214.171.124) and phosphoglucomutase (PGM, EC 126.96.36.199) in the populations. Wild cherry (P. avium) seedlings exhibited greater variation than P. mahaleb. Cherry seedlings had leaf areas ranging from 25.4 to 60.3 cm(2) lsozyme polymorphism was observed in seedling populations of both species at 7 enzyme loci with 35 alleles in total (19 alleles in cherries and 16 alleles in 'Mahaleb'). Isozyme variability was higher in sweet cherries than 'Mahaleb' due to high level of heterozygosity. The study demonstrates the value of clonal rootstocks for eliminating the genetic variability within seedling rootstocks.