<p>We analysed the mechanisms that, together with Mendelian inheritance, may be acting in the maintenance and evolution of colour polymorphism in the Booted Eagle (<i>Hieraaetus pennatus</i>), using observational data from successful breeding events of mixed pairs formed by light morph males and dark morph females, from a long-term study conducted in south-eastern Spain. Our results show that dark offspring produced in breeding events involving mixed-morph pairs far exceed the value expected in the Hardy–Weinberg equilibrium. Two-eaglet broods mostly resulted in one fledgling of each colour morph and in broods in which only one survived, it was predominantly the dark morph, with a ratio of 0.143:1 light/dark. In the two-egg clutches where only one hatched, the resulting eaglet was mostly dark morph with a ratio of 0.167:1 light/dark. Furthermore, three single-egg clutches produced a dark morph eaglet fledgling. However, these biases in embryo viability, chick survival and single clutches accounted for only seven (19.44%) of the 36 dark eaglets obtained. Of the remaining twenty-nine, six (16.67%) were expected according to Hardy–Weinberg equilibrium and twenty-three (63.89%) were produced by disassortative mating, a phenomenon described in previous studies, whereby heterozygous light males preferentially mate with dark females, likely based on the imprint of the colour morph of their mother. This long-term monitoring of breeding events has allowed us to understand the importance of each of the combined phenomena that contributes to the positive bias towards the dark morph in relation to the expected proportion according to the Hardy–Weinberg equilibrium.</p>