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The origin of the putatively autotriploid plant with 2n=3X=24 chromosomes growing in Mediterranean and Near East countries is unclear. As saffron is male sterile and thus vegetatively propagated, it is assumed that there is just one saffron cultivar grown worldwide. Still there are differences in quality and phenotype reported, this being attributed to clonal differences. So far molecular analyses only concentrated on the identification of the putative ancestors of C. sativus L. using RAPD, AFLP, IRAP or ISSR markers, but no extensive study has been conducted to prove the genetic identity and the putative clonality of cultured saffron. In the limited phylogenetic studies conducted so far, C. sativus L. exhibited little to no genetic variation. In our study we concentrated on C. sativus L. exclusively, using maternally inherited choloropalst (cp) markers as well as microsatellite regions contained in expressed genes (EST-SSRs) to investigate genetic diversity. Out of the 6803 available saffron ESTs (D'Agostino et al., http://www.saffrongenes.org) 200 sequences proved to contain SSR regions. Out of these, for 38 sequences primers could be developed and tested on 29 different saffron accessions. In addition to the nuclear SSRs, 8 cp regions were investigated. Due to the fact that none of the regions revealed any genetic difference among the investigated probes, sequencing of 5 genes was conducted in order to identify single base pair mutations in the respective genomic areas.