Two pigmentation genes are often associated with deafness in dogs: the merle gene (seen in the Collie, Shetland Sheepdog, Dappled Dachshund, Harlequin Great Dane, American Foxhound, Old English Sheepdog, and Norwegian Dunkerhound among others) and the piebald or extreme piebald gene (Bull Terrier, Samoyed, Greyhound, Great Pyrenees, Sealyham Terrier, Beagle, Bulldog, Dalmatian, English Setter). Not all breeds with these genes have been reported to be affected with deafness.

The merle (dapple) gene (M) produces a mingled or patchwork combination of dark and light areas. This gene is dominant so that heterozygous dogs (Mm) show the pattern, which is considered desirable in many breeds. However, when two dogs with merle are bred, 25% on average will end up with the MM genotype. These dogs usually have a solid white coat and blue irises, are often deaf and/or blind, and are sterile. Experienced breeders of these dogs know not to breed merle to merle. Heterozygous merles can also be deaf, with the likelihood of deafness increasing with increasing amounts of white in the hair coat. In this case the deafness is neither dominant nor recessive, but is linked to a dominant gene that disrupts pigmentation and secondarily produces deaf dogs.

Genetic transmission of deafness in dogs with the piebald (sp) and extreme piebald (sw) pigment genes, such as the Dalmatian, is less clear. These genes affect the amount and distribution of white areas on the body. The canine piebald genes are recessive, but individuals in breeds such as the Dalmatian are homozygous, so all dogs within the breed express the pigment pattern.

Deafness in Dalmatians does not appear to be dominant since deaf puppies result from hearing parents. It does not appear to be a simple recessive disorder: researchers have bred pairs of deaf Dalmatians and obtained many bilaterally hearing puppies, when all should have been deaf if the disorder was recessive.

These findings might be explained by a polygenic cause, the presence of two different autosomal recessive deafness genes, or a syndrome with incomplete penetrance. Suggestions have been made for two different recessive genes, either of which can cause deafness, or two recessive genes where both are required to cause deafness, or a recessive multifactorial gene with incomplete penetrance.

Deafness is still clearly linked to the extreme piebald gene in Dalmatians. In this breed, the underlying coat colour is black (B) or liver (b, simple recessive). The extreme piebald gene (sw) covers the colour with white, and the dominant ticking gene (T) opens the spots through the white. In Dalmatians with a patch, the sw gene does not completely suppress the underlying coat color; the sw gene is only weakly expressed. Patched Dalmatians have been shown to have significantly lower deafness rates, but a patch is not allowed in the breed standard. Conversely, blue-eyed Dalmatians, where the normal brown iris pigment is suppressed, are significantly more likely to be deaf. Blue eyes are allowed in the breed standard of the United States, but not in Canada or Europe. Efforts through breedings to reduce blue eyes in Norwegian Dalmatians reduced the prevalence of deafness.

Deafness in Dobermans, which do not carry the merle or piebald genes, results from direct loss of cochlear hair cells without any effects on the stria vascularis . Head tilt and circling are often seen, and the deafness is transmitted by a simple autosomal recessive mechanism. A similar pathology has been described for the Shropshire Terrier.

 Numerous references report that most congenital deafness in dogs is autosomal recessive. However, the available research findings suggest that this is not true for most breeds.