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Pepper (Capsicum) is one of the most important and widespread vegetable crops in the Balkans. Some old indigenous forms are not the focus of modern breeding but are preserved in some areas and represent valuable genetic resources. Three Bulgarian varieties (Plovdivska kapiya, Familiya and IZK Delicates) C. annuum, and two representatives of the chili pepper C. chinense and C. frutescens. Interspecific hybrids were made between sweet (C. annum) and chili pepper plants. The genetic relationships of the varieties of Capsicum species were assessed using ISSR primers. PCR amplification of isolated DNA from parental lines and interspecific hybrids revealed 65 distinct polymorphic bands. Cluster analysis clearly distinguished the parental forms and individuals from the F1 and F2 populations. The applied ISSR molecular technique can be successfully used to analyze genetic diversity in cultivars, early-stage seedlings, and interspecific hybrids, as well as to detect differences in individuals whose genomes are highly homogeneous, such as those of the genus Capsicum. [ABSTRACT FROM AUTHOR]