Pepper as a plant with a spicy taste is an important worldwide vegetable. Its spicy taste is caused by a substance called capsaicin, from the group of chemicals named alkaloids, which has a lot of documented and undocumented effects on humans and is unique to Capsicum genus. Recently sequenced pepper genome enables further research in the genus of peppers and its relatives. The use of genetic tools makes a significant contribution to the quality of breeding new varieties of peppers. By using the DNA markers we can determine capsinoid biosynthetic ability of plants. Researchers have discovered the usefulness of SCAR markers for pepper breeding programs and used nucleotide region of sequence hrbouring a deletion present in mild peppers for phylogenetic studies. Developed genetic markers have direct practical value in breeding programs for distinguishing spicy and non-spicy peppers at the seedling stage.