The oxygen affinity of most vertebrate haemoglobins in the absence of diffusible electrolytes is much higher than that of blood. In the red cell this affinity is lowered by organic phosphates, hydrogen ions, chloride ions and CO2 (refs 1–5). Similarly, crocodilian haemoglobin also has a much higher oxygen affinity than crocodile blood, but this is due to bicarbonate ions6, as neither phosphates nor carbamino CO2− lower its oxygen affinity, and chloride does so only weakly7. The complete sequences of the haemoglobins of the caiman, the Nile crocodile and the Mississippi alligator (to be reported elsewhere8) show 102 substitutions between human and caiman, and 123 between human and the other two crocodilian haemoglobins. Here we consider how these substitutions may explain the changes in allosteric control, and also their bearing on the phylogenetic relationships between the crocodilians and other groups of bony vertebrates. We propose that a few of the substitutions abolish or weaken the binding sites for the usual allosteric effectors and create a new pair of binding sites which are complementary to bicarbonate ions in the deoxy (T) structure, but not in the oxy (R) structure.