In this study, a total of 26 Crocus specimens from different locations across Turkey and 2 East Aegean islands (Chios and Samos) were analyzed using 12 amplified fragment length polymorphism (AFLP) primer combinations to obtain information on genetic diversity, population structure, and genetic relationships. A total of 369 polymorphic AFLP bands were generated and scored as binary data. Genetic similarities were determined. Cluster analysis revealed 4 major groups among the 26 genotypes examined in this study. The nuclear DNA contents (2C) of the 26 Crocus specimens were found to range from 5.08 pg in C. asumaniae to 9.75 pg in C. sativus. Polymorphic information content (PIC) values were used to examine the capacity of the various primer pairs to amplify polymorphisms in the Crocus specimens. The PIC values ranged from 0.218 (M-CAA/E-AGC) to 0.512 (M-CAT/E-AAG) and showed an average of 0.34. In sum, we herein used AFLP analysis to identify a high level of polymorphism among Crocus specimens collected from various locations in Turkey and Greece, and our structural analysis yielded 2 reconstructed populations. These findings provide new insight into the relationships among different Crocus genotypes and show that AFLP analysis can be useful for Crocus diversity studies.