Mulberries (Morus L.) show a great deal of genetic variability and adaptability to various environments. There are more than 24 species of mulberries in cultivated and wild forms. In Turkey, three Morus species, M. alba L., M. nigra L., and M. rubra L., are grown. In this study, we attempted to characterize 43 Morus accessions originating from distinct regions of Turkey using fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis. The accessions belonged to M. alba, M. nigra, and M. rubra; M. alba consisted of white- and purple-fruited samples. Eight primer combinations generated a total of 416 bands, 337 of which were polymorphic (80.5%). Resolving powers of the AFLP primers ranged from 0.410 to 0.942 making a total of 5.015, whereas the polymorphic information content ranged from 0.662 to 0.898 with an average of 0.812. Unweighted pair-group method of arithmetic mean (UPGMA) clustering of the accessions showed three major groups representing M. nigra, M. rubra, and M. alba accessions. The M. alba group had two subgroups that were not correlated with fruit color. The UPGMA dendrogram of average taxonomic differences confirmed these results. The principle coordinate analysis demonstrated that M. nigra accessions had limited genetic variation. In conclusion, our study indicated that M. nigra and M. rubra are molecularly distinct from M. alba. Our results also suggest that M. nigra accessions having a low level of morphological variation are molecularly similar.