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The pepper (Capsicum annuum L.) is very popular annual vegetable either for fresh consume either as spice after drying and grinding. The fruit contains high amounts of vitamin C, provitamin A, E, P (citrin), B1 (thiamine), B2 (riboflavin) and B3 (niacin). Crop Research Institute (CRI), Department of Ve­ge­ta­ble and Special Crops, Olomouc, the Czech Republic is the holder of the collection of pepper genetic resources. The collection of pepper consists of 504 accessions, currently. It is necessary to find duplications within collection for effective work with genetics resources. For analyses totally 41 accessions were chosen. These were divided into ten groups according name: 1. Astrachanskij, 2. Aufrechte Cayenne, 3. Bogyisloi, 4. Hatvani, 5. Japan Hontakka, 6. Japan Madarszen, 7. Kalocsai Fuszer (Edes), 8. Konservnyj Belyj 289, 9. Tetenyi and 10. Vinedale. Two approaches were used for the detection of duplications – morphological description and polymorphism of DNA. The accessions were characterized for 54 morphological traits: 1 character in seedlings, 8 characters in the plants, 10 characters in leaves, 10 characters in flowers and 25 characters in fruits. The polymorphism of DNA was analysed using the SSR (Simple Sequence Repeats) method with 8 SSR markers (Hpms 1-1, Hpms 1-5, Hpms 1-168, Hpms 1-172, Hpms 1-274, Hpms 2-21, Cams 163 and Cams 647) which are localised on different chromosomes. The results from DNA analysis were complemented with the morphological characterization. Possible duplications were in 4 groups: 1. Astrachanskij, 4. Hatvani, 5. Japan Hontakka and 7. Kalocsai Fuszer (Edes). This work is the first step for the determination of duplications in the Czech germplasm collection of pepper.