The genetic relationships among 14 Turkish pepper (Capsicum annuum L) genotypes, 6 of them inbred lines, were determined by comparing their molecular traits. The taxonomic relationships and genetic variation among these genotypes were investigated with those of 5 foreign pepper genotypes. Fifty-six (26%) polymorphic AFLP markers out of total 215 DNA fragments from 4 primer pairs were used to define the genetic similarity among the pepper genotypes by dendrograms or two and three dimensional scaling. Two genotype-specific markers for the genotype PM-702 were among the polymorphic ones. The inbred lines of Alata Agricultural Research Institution were partitioned to similar clusters and constituted extremely low genetic variation. On the other hand, other local Turkish genotypes had comparatively higher genetic diversity.