Toy and Mini Aussie Breed Eye Color 
Eye Colors found in the Toy and Miniature Australian Shepherd 
The Toy and Mini Aussie breed standard allow eyes of any pigment color or combination of pigment colors. 
Aussie eyes have been seen that are golden, lemon yellow, amber, light brown, dark brown, green, orange, and blue. 
Blue-eyed Toy and Mini Aussies are highly sought after in both the merle and tri-coat colors. If you are looking for a working dog that will be out in the bright sun for hours at a time, we here at Toy Mini Aussies do not recommend a blue-eyed dog. Blue eyes lack pigment which seems to be more sensitive to bright light. This makes the dog squint, reducing his field of vision. 
Below are some examples of the extraordinary variety of eye colors we find in this breed.
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When a dog’s iris contains two or more colors, the medical term is heterochromia iridis. If the irises of his eyes are different from each other (one blue/one brown, etc) the term is heterochromia irides. Common terms for two eyes different from each other include odd-eyed, walleyed, glass-eyed. In domestic mammals, having one pigmented eye and one blue eye is not uncommon. It’s been observed in horses, donkeys, cattle, water buffalo, cats, ranched foxes, and dogs.
Close up of Heza Hoots eyes - an example of flecked eyes.
This is Shade Tree Aussies CH PC Heza Hoot, a blue merle male.
Notice the blue fleck in both eyes.
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An example of blue eyes in merle Toy Aussies. Shown here is Sheza Blue Eyed Donna and Heza Blue Eyed Rascal.

On the left: Shade Tree Aussies CH PC Sheza Blue Eyed Donna
On the right: CH Heza Blue Eyed Rascal

*The sire CH PC Heza Hoot’s eyes are shown in the first picture on the page. Both Donna and Rascal’s dams (mothers) were dark-eyed dogs. Yet as you will note, Donna and Rascal both have bright blue eyes.
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Blue Eyed Tris
The presence of blue eyes does not always indicate a merle. This type of recessive blue eye can be observed both in merles and nonmerles. In Aussies, recessive blues like this are caused by a recessive gene similar, to that found in Siberian huskies and Border collies. Recessive blues can be entirely blue, like Kibby’s, or they can be geometrically split. This gene does not cause marbling. If a blue merle has solid blue or geometrically split blue, it’s not really possible to tell by appearance alone whether the blue eyes are due to this recessive gene or due to the effects of merling. 
An example of a blue-eyed black tri. This is CH PC Timberlines Miss Kibby.
A true blue-eyed black tri. This is Shade Tree Aussies CH Timberline Missy Kibby.
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Marbled Eyes or Split Eye Color
Note the eye shown on the right side of the picture is split or marbled. There is nothing wrong with this eye or the dog's vision. This is often found in merle Aussies. 
An example of split or marbled eyes. This is All That Jazz of Shade Tree Aussies.
An example of split or marbled eyes. This is All That Jazz of Shade Tree Aussies.
There is a recessive gene in some strains of Aussie that produces blue eyes independently of merling (blue-eyed black or red tri, commonly noted with BET). It can produce a dog with two blue eyes, one blue and one pigmented, or irises that are split. Generally, these eyes are split geometrically, not marbled. Of course, a blue-eyed merle puppy in such a litter may also be expressing this recessive trait and may not have blue eyes simply as part of the action of the merle gene like most blue-eyed merles. There is some relationship between eye color and coat color.
Another example of two different colored eyes. This is Heza Moose.
This puppy displays eyes of two different colors. This is Shade Tree Aussies Heza Moose.

The two eyes of one dog are not always both the same color; one may be pigmented while the other eye is blue, or both may be pigmented but be of different colors (heterochromia irides).

Effects of Coat Color on Eye Color
There are probably multiple genes that together affect eye color and it is not possible to predict with certainty eye color from planned breeding. As a generalization, brown eyes tend to be dominant over lighter eyes. There is some relationship between eye color and coat color as well since black pups will tend to have slightly darker eyes than red pups in the same litter.
At the back of the eye, there is a layer of reflective pigment called the choroid layer. This mirror-like layer reflects available light and allows dogs to see well even in very dim light. In an eye with normal pigmentation, the eye reflects a silvery greenish color in bright light. In eyes lacking pigment, the eye reflection is red. Some dogs will have one of each. This layer is responsible for eyeshine in cats as well. 
For more information about eyes, eye color and eyeshine, please visit the Australian Shepherd Health and Genetics - ASHGI 
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