Molecular technology has led to the discovery of previously unrecognized Cryptosporidium species in new hosts, such as C. canis in humans. The notion that dogs may transmit Cryptosporidium species to humans has significant public health implications, and additional studies are merited. The purpose of this study was to examine a group of kenneled dogs to determine the prevalence of Cryptosporidium species infection and to identify parasite species. Prevalence of active infection was 71%. Six positive samples were analyzed by polymerase chain reaction amplification of the 18S ribosomal RNA gene followed by restriction fragment length polymorphism analysis to identify the Cryptosporidium species. Restriction digest patterns identified C. muris as the infecting species in all six dogs; species identity was confirmed by genetic sequencing. To our knowledge, this is the first report of a naturally occurring C. muris infection in a canine host. The finding of C. muris in asymptomatic canines supports the notion of dogs as potential sources of human infection.