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Mitochondrial respiratory chain Complex III, also known as cytochrome <i>bc</i>₁ complex or cyt <i>bc</i>₁, is a validated target not only for antibiotics but also for pesticides and anti-parasitic drugs. Although significant progress has been made in understanding the mechanisms of cyt <i>bc</i>₁ function and inhibition by using various natural and synthetic compounds, important issues remain in overcoming drug resistance in agriculture and in evading cytotoxicity in medicine. In this review, we look at these issues from a structural perspective. After a brief description of the essential and common structural features, we point out the differences among various cyt <i>bc</i>₁ complexes of different organisms, whose structures have been determined to atomic resolution. We use a few examples of cyt <i>bc</i>₁ structures determined via bound inhibitors to illustrate both conformational changes observed and implications to the Q-cycle mechanism of cyt <i>bc</i>₁ function. These structures not only offer views of atomic interactions between cyt <i>bc</i>₁ complexes and inhibitors, but they also provide explanations for drug resistance when structural details are coupled to sequence changes. Examples are provided for exploiting structural differences in evolutionarily conserved enzymes to develop antifungal drugs for selectivity enhancement, which offer a unique perspective on differential interactions that can be exploited to overcome cytotoxicity in treating human infections.