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Papaver bracteatum Lindl., P. orientale L., and P. pseudo-orientale (Fedde) Medw., species of section Oxytona Bernh. in the genus Papaver L., are found widely in the native flora of Turkey. They are commercially important for their high alkaloid content. Because genus Papaver section Oxytona has similar morphological characters, it is not easy to distinguish these species. We used the inter-simple sequence repeat (ISSR) molecular marker system to determine the molecular characterisation of this section. In this study, 20 ISSR primers have been studied in 180 accessions collected from 5 different regions of Turkey. A total of 82 bands were obtained, of which 80 were polymorphic. Average genetic distance was found to be 0.35, the Shannon index was 0.50, and the polymorphism rate was 96.97%. The primer AT10 had the smallest number of bands, which was 3, while the primers AT19 and AT3 had the greatest number of bands, which was 5. In conclusion, the ISSR marker system can be used for the classification of section Oxytona.