The molecular characterization of cultivated plant genepools is of foremost importance for germplasm utilization in plant breeding. However, no comprehensive genetic fingerprinting of Turkish lentil landraces existed so far. To overcome this gap, 38 lentil landraces from southeast Turkey, together with six commercial varieties, were molecularly characterized using inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) molecular markers. The ISSR analysis, performed with 14 primers, yielded 105 polymorphic bands and the AFLP analysis, carried out with six primer combinations, amplified 119 polymorphic fragments. Even though the AFLP produced more bands per primer combinations, the ISSR detected more polymorphisms. Unweighted pair-group method with arithmetic means dendrograms based on Jaccard similarities obtained from three data sets: (i) ISSR, (ii) AFLP and (iii) combined ISSR and AFLP data, were similar and separated the landraces into two main groups. Turkish lentil landraces exhibited considerable genetic diversity. One landrace from Karacadag/Diyarbakir region was significantly different from the rest of the germplasm analysed. Jaccard distances highlighted sharp differences among landraces over short geographic distances. The knowledge of regional differentiation has practical utility in the management of germplasm and in breeding programmes.