Series Crocus comprises ten autumn-flowering species, including the cultivated Crocus sativus, Saffron-Crocus. Interspecific genetic variation was examined in all species of the series, except for C. naqabensis. Intraspecific genetic and morphological variation was considered in the three Greek endemics, C. cartwrightianus, C. hadriaticus and C. oreocreticus. Genetic variation was evaluated based on amplified fragment length polymorphism and simple sequence repeats analyses, including 94 and 233 specimens, respectively. Analysis of molecular variance demonstrated significant genetic variation within populations, compared with low genetic variation between populations suggesting substantial gene flow between populations. In Neighbour-Net analysis, C. hadriaticus samples from mainland Greece were separated from Peloponnesian samples; C. cartwrightianus, C. hadriaticus and C. oreocreticus generally were grouped with C. sativus samples. Pollination and maintenance of genetic variation are discussed. The large intraspecific variation found within the three specifically studied species reflects dynamic population structures with potential to meet future ecological fluctuations. It emphasises a large gene pool which should be considered by including a larger number of accessions in genetic diversity studies.