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Mandarins are the second most farmed citrus. Consumers demand a mandarin fruit that is both tasty and excellent in quality. The fruit quality, flavonoid profile, antioxidant capacity and total carotenoid content of five varieties (‘Zorica’, ‘Chahara’, ‘Kawano Wase’, ‘Owari’ and ‘Saigon’) of Satsuma mandarins grown in Neretva valley (Croatia) were determined. In this research, the distribution of bioactive compounds was different for mandarin juice, dry pulp residue and dry peels. Dry peels showed higher levels of polyphenolic compounds and antioxidant activity. Total carotenoids were found to be in a greater concentration in dry pulp residue than in the dry peel. The highest levels of total carotenoids (543 μg β-carotene/g) were found in the dry pulp residue of ‘Owari’ and ‘Saigon’, while the lowest levels were in ‘Chahara’ (227.87 μg β-carotene/g). In dry mandarin peels, the highest levels of total carotenoids were in ‘Kawano Wase’ (227.58 μg β-carotene/g), and the lowest levels were in ‘Chahara’ (52.24 μg β-carotene/g). The most abundant component of polymethoxyflavones (PMFs) in mandarin dry peel was nobiletin, ranging from 0.204 mg/g (‘Chahara’) to 0.608 mg/g (‘Saigon’), followed by tangeretin, ranging from 0.133 mg/g (‘Chahara’) to 0.251 mg/g (‘Saigon’), and sinesestin (‘Zorica’), ranging from 0.091 mg/g to 0.353 mg/g (‘Saigon’).