Why Do Some Dogs Have Blue Eyes? The Genetics Explained

Most dogs have brown eyes. Blue eyes come from at least three genetic routes: a duplication near the ALX4 gene that's common in Siberian Huskies, the merle coat pattern, and white markings that extend over the eyes. The same routes explain heterochromia, when a dog has one blue eye and one brown, or a slice of blue within a brown eye.

The short version

• Brown is the usual eye colour in dogs.
• The husky route: a duplication of DNA next to the ALX4 gene, largely found in Siberian Huskies, is strongly linked to blue eyes.
• The merle route: merle dilutes pigment in patches, and when a patch reaches an eye, that eye can be blue or partly blue.
• The white-marking route: extensive white markings that reach the eyes can do the same, though only in a small share of white-marked dogs.
• Heterochromia (two different eye colours) can come from any of these routes.
• Merle has been linked to hearing and eye problems in some dogs, so ask your vet if you have concerns.

The husky gene: a duplication near ALX4

Siberian Huskies are famous for blue eyes, and a 2018 study found why. Using more than 3,000 dogs, plus validation panels of nearly 3,000 more, researchers found a strong link between blue eyes and a 98.6-kilobase duplication of DNA just upstream of ALX4, a gene with an important role in eye development.

The duplication is largely restricted to Siberian Huskies and is strongly associated with blue eyes, but not every dog that carries it has them. The researchers also found it was associated with blue eyes in non-merle Australian Shepherds, and the study's title links it to heterochromia in huskies too.

Merle and blue eyes

Merle is a coat pattern of diluted, patchy colour, caused by an insertion in a gene called SILV, also known as PMEL. A 2006 study identified the merle gene in Shetland Sheepdogs and found the same insertion in merle dogs of several breeds.

When the diluted patches extend across the face, they can reach the eyes. As the 2018 husky study explains, merle and white-spotting genes can lead to one or two blue eyes, or slices of blue within an eye, when depigmented areas extend across the face. That's why merle breeds such as the Australian Shepherd often have blue or partly blue eyes.

The same 2006 study linked the merle gene to a range of hearing and eye problems in some dogs. Blue eyes alone aren't a diagnosis of anything, but if your dog is merle and you have any concerns about its hearing or eyes, talk to your vet.

White markings and blue eyes

White patches in a dog's coat come from white-spotting genes. A 2007 study mapped the major white-spotting gene to MITF. When white markings extend over the eyes, the eyes can lack pigment and look blue. The husky researchers noted that piebald white spotting causes blue eyes in only a small share of cases, so most white-marked dogs still have brown eyes.

Heterochromia: two different eye colours

A dog with one blue eye and one brown has complete heterochromia; a dog with a slice or patch of blue in a brown eye has sectoral heterochromia. Both can come from any of the three routes: the husky duplication, merle or white markings. In each case, the difference comes down to where pigment did or didn't reach as the eye developed.

Blue eyes in puppies

Many puppies' eyes look blue-grey at first and settle into their adult colour as they grow, so a young puppy's eye colour isn't the final word. If you're curious whether blue eyes will last, a DNA test can show whether a puppy carries the husky-type duplication, and its coat pattern can hint at the other two routes.

How a DNA report shows eye colour

The PuppyGenes physical appearance section includes an eye colour prediction based on ALX4, the husky-type route. It covers that one tendency, not every possible eye colour. Juno, one of our public example reports, is predicted to be "less likely to have blue eyes" at high confidence. Merle, a separate route, belongs to the coat colour section, where it's reported when the sample supports it; in some samples it can't be determined. Our guide to reading a dog DNA report explains how confidence and undetermined results work.

Huskies and other cold-weather breeds share more than eye colour; our guide to the best dogs for Canadian winters covers why their coats suit the cold.