Potato virus Y (PVY) is the type member of the genusPotyvirus (family Potyviridae), the largest group of RNA plant viruses. PVY isolates were collected according to hierarchical (nested) sampling design. Collections were made in 100 fields in seven localities in Hatay, thirteen localities in Kahramanmaras (Eastern Mediterranean) and seven localities in Gaziantep (Southeast Anatolia). DAS-ELISA revealed the infection of 167 samples with PVY from a total of 1098 pepper (Capsicum annuum) plants showing symptoms of viral infection. Genetic diversity among these 167 samples was examined by RT-PCR-RFLP analysis of coat protein (CP) cistron. The entire CP cistron was amplified using polyvalent primers for all PVY groups and amplified a 1159 nucleotide fragment. Two restriction endonucleases (HaeIII and MseI) used for RFLP analyses of RT-PCR products were chosen based on genomic sequences available for PVY group C, which includes almost all pepper isolates. RT-PCR-RFLP analyses revealed between two and four DNA profiles. Conseuently, only 85 of the 167 PVY positive samples from Hatay were analysed for CP genome segment and they all had the diversity. None of the samples from all other localities had the diversity.