The Root effect describes an extreme pH sensitivity expressed in the hemoglobins of certain fish, in which it plays a unique physiological role. This review describes our general understanding of the effect of protons on the oxygen binding properties of hemoglobin and the particular properties which characterize Root effect proteins. The development of our understanding of the molecular origins of this effect is outlined and the role played by our ever expanding knowledge of protein structure is highlighted. The present state of our knowledge is detailed.