Why Do Australian Shepherds Have Blue Eyes? The Science & Meaning

The Australian Shepherd — affectionately called the “Aussie” — is a family favorite known for its intelligence, agility, and loyal personality. But perhaps nothing about this breed is more visually striking than its piercing blue eyes.

At Mawoo Pets, we’ve helped thousands of families adopt Aussies and Aussie mixes, and we’ve heard the same question again and again: Why do Australian Shepherds have blue eyes?

In this article, we’ll break down:

• What causes blue eyes in Aussies

• Why some Aussies have one blue eye and one brown

• Whether blue eyes are linked to health risks

• What eye colors Aussies can actually have

Let’s get into the science behind those mesmerizing Aussie eyes.

What Makes an Aussie's Eyes Blue?

You might be surprised to learn that blue eyes are not in fact blue. Rather, they are eyes with low pigmentation, which causes light to scatter in the eye and appear as blue when seen. 

This concept is similar to why the sky appears blue: when sunlight hits gases in the sky and scatters, we see the blue light first and most prominently, because it has the lowest wavelength and travels most easily.

So, when you see a blue-eyed Aussie, you're really seeing low-pigment eyes, not blue pigment itself. It’s a visual illusion backed by biology — and genetics.

Here are blue eyes in some of our puppies:

Non-Merle Aussie with Blue EyesMerle Aussie with One Blue EyeMerle Aussie with Two Blue Eyes

What Causes Blue Eyes in Aussies? 

The main factor leading to the blue color of Australian Shepherd eyes is genetics. Specifically, the Merle gene is what typically causes patches of low pigmentation – in fur or eyes. 

On the skin of an Aussie, this can be seen as white patches which gives some Aussies a distinctive “patchy” look. The same Merle gene which dilutes the coat color also reduces pigmentation in the eye – in one eye, or both eyes. 

Not all blue-eyed Aussies have the Merle gene, though. Other genetic factors — still being studied — can also cause blue eyes, even in non-Merle dogs. This is why you may also see non-Merle Aussies with blue eyes. 

Why Do Some Aussies Have Two Different Colored Eyes? 

The phenomenon where a dog (or a person) has differently colored eyes is called heterochromia, and it's common in Australian Shepherds.

When pigments are expressed in a given region of the body, different genes may be expressed. It’s for this reason that a Merle Australian Shepherd won’t be entirely white, but rather have patches of white, brown, black, etc. This depends on what genes are expressed in that patch of skin. 

It’s the same story for the eyes. One eye can have the light-pigmentation genes expressed, while the other eye doesn’t express those genes. This leads to one eye being blue, and the other being a different color like brown. 

Do All Australian Shepherds Have Blue Eyes? 

Nope! While it’s a common trait, not all Aussies have blue eyes. They can also have brown, hazel, amber, green, or mixed/marble eyes.

According to the AKC breed standard for Australian Shepherds, acceptable eye colors include:

“Brown, blue, amber, or any variation thereof—including flecks and marbling. All are equally acceptable.”

It’s not uncommon for Aussies to have split eyes (half blue, half brown) or heterochromia (each eye a different color

Common Eye Colors in Aussies:

Are Blue Eyes a Sign of Bad Health? 

Blue eyes on their own are not a sign of poor health. However, blue eyes may stem from the Merle gene which is linked to genetic health issues. So, is this something you should be worried about? 

If an Aussie carries the Merle gene, they may carry a single or double allele (i.e. one or two copies of the Merle gene). The presence of the Merle gene can lead to blue eyes, even if only a single allele is present. It’s a dominant gene. 

One Merle gene typically doesn’t cause health issues. But having two Merle genes – also called being “double Merle” – can lead to genetic health issues, typically hearing and vision issues. This can result from breeding two Merle-patterned Aussies, which can result in offspring that carry two copies of the Merle gene. 

This is why ethical breeders avoid pairing two Merle-patterned Aussies. If you're buying or adopting, be sure to ask if the puppy is from a Merle-Merle pairing.

Quick Facts About Aussie Eye Colors

• ✅ Not all Aussies have blue eyes

• ✅ Blue eyes are caused by low pigmentation, often due to the Merle gene

• ✅ Heterochromia is common and harmless

• ✅ Eye color can change as puppies grow

• ⚠️ Double Merle Aussies are at risk for hearing and vision issues

Do Aussie Mixes Like Aussiedoodles Have Blue Eyes?

Yes! Pups like Aussiedoodles, Aussie Labs, and other crosses can inherit blue eyes — especially if one parent carries the Merle gene. However, eye color in mixed breeds is more variable and less predictable.

Conclusion

The Australian Shepherd is a loving family companion that is also excellent with kids. But what typically stands out about them visually is their fur pattern and eye colors. Specifically, many Aussies sport patterned fur and blue eyes. 

The blue eye of the Australian Shepherd can be caused by the Merle gene, but can result from other genetic factors as well, which continue to be studied by canine researchers.

The genes can be expressed in one or both eyes, resulting in one or both eyes being blue. Additionally, while the Merle gene is not necessarily dangerous, two copies of it can cause health issues – so it’s best to avoid breeding two Merle Australian Shepherds, as their offspring may carry two copies of the Merle gene and have health issues. 

FAQs about Australian Shepherd's Blue Eye Color

Do all Australian Shepherds have blue eyes?

No, not all Aussies have blue eyes. Their eye colors can range from blue, to green, hazel, yellow, and brown -- with the possibility of one eye being one color and another a different color due to to heterochromia.

Why do some Australian Shepherds have two different colored eyes?

This is due to heterochromia, a condition where each eye is a different color. This happens because the genes responsible for pigmentation are expressed differently in each eye, resulting in one eye being one color, such as blue, and the other being a different color, such as brown.

Will an Australian Shepherd puppy keep its blue eyes?

Not necessarily! While many Australian Shepherd puppies are born with blue eyes, the eye color can change as they grow older, because the pigmentation can change. You can determine your Aussie's adult eye color after the first few months of their life.

Can other breeds like German Shepherds have blue eyes?

Yes, they can. It's less common for a breed like the German Shepherd, and it's not in their breed standard, but German Shepherds or German Shepherd mixes can have blue eyes. This would happen because of a genetic mutation or the eye color being inherited from a mix with another breed that carries the blue eye genes.