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Breeds That Include the Merle Pattern in Their Official Standard

Documented Historically Merle Breeds 

Alapaha Blue Blood Bulldog 

American Leopard Hound (referred to as "Leopard")

Australian Koolie (German Coolie)

Australian Shepherd

Beauceron (referred to as "Harlequin")

Bergamasco

Berger des Alpes et de Savoie

Border Collie

Cardigan Welsh Corgi

Catahoula Leopard Dog (referred to as "Leopard")

Collie - Rough and Smooth

Cuban Hairless Terrier

Dachshund (referred to as "Dapple")

Dunker/Norwegian Hound

Great Dane

Harlequin Pinscher

Mudi

Miniature American Shepherd

Old English Sheepdog
(The trait seems to be absent from the modern gene pool.)

Prague Ratter

Pyrenean Shepherd (may be referred to as "Harlequin")

Shetland Sheepdog

Breeds with the Merle Trait more recently added (via another breed)
and accepted in the AKC Standard
FCI Standards Do Not Allow for the Merle Trait in These Breeds

Chihuahua

Pomeranian

Merle Trait is present in the breed; can be registered but is disqualified for showing.

Teddy Roosevelt Terrier