Colour polymorphism occurs in several animal taxa and in around 3.5% of bird species. This phenomenon is disproportionately high in raptors, affecting approximately 30% of species. However, there are only four research studies in wild Accipitridae species and two in Falconidae species on colour plumage polymorphism. Here, we used the data collected over 23 years (1995‐2017) for non‐tagged individuals of three Spanish Booted Eagle (Hieraaetus pennatus) populations in order to evaluate the stability of morph frequencies during the study period, also for each sex and between sexes, and also the inheritance pattern of colour plumage polymorphism. Our results showed that morph ratios appeared stable over time and between sexes. In one of the studied populations, we found a biased proportion between dark males and dark females, with very few dark males. Our results suggest that this species follows the typical Mendelian inheritance pattern, the light allele being dominant, for which we propose a system involving two loci with epistasis and two alleles per loci. This system would explain all the cases of colour morphs observed in our studied populations and also that described in the main raptor identification guides. Although our results showed no sex‐linked morph inheritance, the offspring produced in mixed pairs with light males and dark females appear significantly linked to the colour morph of the female with a ratio 1:1.49 light/dark, contrarily to the ratio of 4.35:1 predicted by the Hardy‐Weinberg equilibrium equation. This fact suggests a transmission ratio distortion (TRD) phenomenon in heterozygous light morph males. Further investigation using molecular genetic markers will be necessary to check the genotypes of breeding adults and their offspring to confirm the inheritance mechanisms operating in this species.