Citrus species are one of the world’s popular fruit crops, cultivated all over the world for their economic and nutritional values. Citrus, like other fruits and vegetables, are an important source of several antioxidant molecules (polyphenols, ascorbic acid, and carotenoids) that can inhibit the harmful effects of free radicals on the human body; due to their functional values and health-promoting properties, Citrus species are considered valuable fruits not only in agri-food industry, but also in pharmaceutical industry. Flavonoids are among the major constituents of polyphenols found in different parts of Citrus fruits (skin, peels, seed, pulp membrane, and juice). Flavonoids have different biological properties (antiviral, antifungal, and antibacterial activities). Several studies have also shown the health-related properties of Citrus flavonoids, especially antioxidant, anticancer, anti-inflammation, anti-aging, and cardiovascular protection activities. In the present review, attempts are made to discuss the current trends of research on flavonoids in different Citrus species.