Previous research in animal shelters has determined the breeds of dogs living in shelters by their visual appearance; however the genetic breed testing of such dogs is seldom conducted, and few studies have compared the breed labels assigned by shelter staff to the results of this testing. In the largest sampling of shelter dogs' breed identities to-date, 459 dogs at Arizona Animal Welfare League & SPCA (AAWL) in Phoenix, Arizona, and 460 dogs at San Diego Humane Society & SPCA (SDHS) in San Diego, California, were genetically tested using a commercially available product to determine their breed heritage. In our sample, genetic analyses identified 125 distinct breeds with 91 breeds present at both shelters, and 4.9% of the dogs identified as purebreds. The three most common breed signatures, in order of prevalence, American Staffordshire Terrier, Chihuahua, and Poodle, accounted for 42.5% or all breed identifications at the great grandparent level. During their stay at the shelter, dogs with pit bull-type ancestries waited longer to be adopted than other dogs. When we compared shelter breed assignment as determined by visual appearance to that of genetic testing, staff at SDHS was able to successfully match at least one breed in the genetic heritage of 67.7% of dogs tested; however their agreement fell to 10.4% when asked to identify more than one breed. Lastly, we found that as the number of pit bull-type relatives in a dog's heritage increased, so did the shelter's ability to match the results of DNA analysis. In total when we consider the complexity of shelter dog breed heritage and the failure to identify multiple breeds based on visual identification coupled with our inability to predict how these breeds then interact within an individual dog, we believe that focusing resources on communicating the physical and behavioral characteristics of shelter dogs would best support adoption efforts.