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Genetic variability among 41 accessions of red pepper (Capsicum annuum L.) was assessed using eight microsatellite markers. Three of the microsatellite markers (Hpms 1-1, Hpms 1-168, and Hpms 1-274) had uniform spectra in all the analyzed plants. Two to eight alleles were detected for the remaining loci. In total, 28 alleles were detected, i.e. 3.5 alleles per one microsatellite locus on average. The highest number of different alleles was detected with Hpms 1-5 (8 alleles) and Hpms 2-21 primers (7 alleles). Molecular data were complemented with morphological measurements according to the descriptor list for the genus Capsicum. A dendrogram based on our genetic analysis suggests a high level of similarity between some of the accessions presumed to be distant and, at the same time, genetic variability between accessions of the same or similar name. These results show the possibility of duplicities in the current Czech collection of red pepper genetic resources.