The study of phylogenetic relationships between 14 Colchicum taxa spread throughout Turkey was performed using a fluorescent-based amplified fragment length polymorphism (AFLP) technique. Five primer pair combinations were used in AFLP reactions. The data set was analyzed statistically using the NTSYS 2.1 software, and the neighbor-joining and maximum parsimony methods were implemented to generate phylogenetic trees. These analyses clustered the samples into 3 main clades. Both the neighbor-joining and maximum parsimony analyses resulted in similar topologies. Furthermore, supporting the phylogenetic trees, a similar grouping of 14 taxa was generated by principal component analysis. The AFLP analysis with 5 primer combinations was carried out to assess 14 taxa. Fragment sizes ranged from 54 to 462 bp in length for each primer combination. The average was 166 fragments per primer pair, primer B2 generated the highest number of bands (200), and primer B3 produced the lowest number of bands (112). A total of 834 polymorphic bands were scored. The cophenetic correlation coefficient between the data matrix and the cophenetic matrix for AFLP data was 0.72. Based on this molecular data, we concluded that the genetic diversity among these Turkish accessions is relatively high.