Pepper, a member of the Capsicum genus of the Solanaceae family, is an annual, cultivated plant that grows in temperate climates. The main analogs of capsinoids, which are the secondary metabolites of peppers, are capsaicin and dihydrocapsaicin. During process, calyxes and peduncles are considered to be waste. Levels of capsinoids in these tissues in not well known. An optimized method was used to extract bioactive materials from the waste products from C. annum L. genotypes. Calyxes and peduncles were collected and dried in the shade. Extractions were in MeOH solutions and the extracts were analyzed using high-performance liquid chromatography (HPLC) to quantify the total amount of capsinoid, capsaicin, and dihydrocapsaicin contents. Capsinoid, and its analogs, were identified in all genotypes at varying concentrations, and their capsaicin and dihydrocapsaicin contents evidenced with liquid chromatography-mass spectrometry (LC-MS). In conclusion, the highest amount of capsinoids was found in chili Samandağ peppers, whereas the lowest amount of capsinoids was found in the red sweet pepper sample. All pepper genotypes, the capsaicin amount was higher comparison to dihydrocapsaicin. Capsanoids and anologues obtained from waste pepper can be used as raw materials in production of value added products.