Heterochromia
When a pup has two different colored eyes, it's called heterochromia. This literally means two different colors. While it can occur in humans, it's not very common. It's much more common in dogs, cats and horses. The distribution of melanin in the iris determines eye color. More melanin means he'll have a darker eye, like brown. Less melanin results in green or blue eyes.
Heterochromia can also cause one eye to lack melanin altogether. When his two eyes have different amounts of melanin, they'll be two different colors. The most common combinations include brown, blue and white.
Causes
Heterochromia is an inherited disorder. This means he got the genes from his mom and dad. Some diseases or an injury to your puppy's eye can cause it to change color and lead him to have two different colored peepers. If he's had the two different colors since he was born, the cause is most likely genetic.