An RT-nPCR assay was used for testing fecal samples of dogs, foxes, raccoon dogs and minks for the presence of canine coronavirus (CCV). The animals were raised in homes, dog schools or farms. Seventy out of 81 healthy dog feces from three cities and 21 out of 48 diarrhea feces from pet dogs were positive for type II CCV. From a total of 61 healthy fox feces, 43 were positive for type II and 29 for type I CCV, out of which 25 were simultaneously positive for the two different genotypes. Among 24 raccoon dogs samples, 22 were CCV type II-positive, and from those 16 were additionally type I positive. No CCVs was detected from healthy mink feces. Sequence analysis found that ten type II CCVs fragments of M gene shared a high similarity with reference strain CCV 1-71 (96.5-99.5%), and four type I CCVs shared a high similarity (96.7%-98.1%) with a reported FCV-like CCV strain. The sequence of one particular M gene fragment was found to cluster between the type I and type II CCV branches in phylogenetic analysis, suggesting the existence of a novel strain. Our study confirmed that type II CCVs infection is very common in domestic dog, fox, and raccoon dog populations in China. This is also the first report on the co-existence of two CCV genotypes in healthy foxes and raccoon dogs.