Canine enteric coronavirus (CECoV) is one of the most common causes of gastrointestinal disorders in dogs, especially unvaccinated young dogs. This study was designed to determine the infection rate of CECoV in the dogs by reverse transcriptase-polymerase chain reaction (RT-PCR) with phylogenetic analysis. Rectal swabs were collected from 211 dogs presenting at Baghdad Veterinary Hospital and private veterinary clinics with clinical signs of gastrointestinal disturbances during the period from February 2022 to June 2023; their ages ranged from 3 months to 7 years. Clinical and demographic data was recorded for each sample, including the dog's number in the household, signalment, with detailed clinical examinations, and diarrhoea's recent history. The molecular results revealed that 13 positive samples (6.2%) were detected; interestingly, seven of the infected dogs from three different households were aged less than 6 months. All the positive samples were classified as CECoV type Ⅱ based on M gene analysis. The phylogenetic analysis results showed that the isolates of this study were closely related to CECoV universal isolates that were isolated from dogs with 98.37–97.02% identity. No previous study was conducted about the detection of CECoV in Iraq.