Since 1925, more than 100 wheat varieties were developed and released in Turkey, and many more were introduced from abroad, but no systematic analysis of their genetic diversity has been performed yet. In this research, a total of 34 domestic and foreign cultivars (12 durum and 22 bread wheats), released in Turkey between 1936 and 2000, were fingerprinted by means of five amplified fragment length polymorphism and three selective amplification of microsatellite polymorphic loci (SAMPL) primer combinations, to evaluate their genetic variation and to determine the existence of cultivar-specific bands. Among the 344 amplicons scored, 214 were polymorphic. The primer combination E-ACG/M-AGG yielded the highest number and the primer combination SAMPL-6/M-AGA produced the lowest number of polymorphic bands. Most cultivars were molecularly very similar, although a few distinct ones (the durum wheat 'Kunduru-1149' and the bread wheat 'Ikizce-96') were also identified. Seven cultivar-specific markers for different bread wheat cultivars ('Golia', 'Seri-82', 'Adana-99', 'Pandas' and 'Sertak-52') and six cultivar-specific markers for durum wheat cv 'Kunduru' were observed. Our results show that genetic diversity among old and present-day wheat cultivar commonly grown in Turkey is limited.