Babesia gibsoni is increasingly recognized globally as a cause of canine tick-borne anemic disease; however, only a few clinical reports of naturally acquired infection are available. In this systematic study of dogs presenting with B. gibsoni infection, clinical and laboratory data were collected for dogs with PCR-confirmed B. gibsoni infection admitted to the National Taiwan University Veterinary Teaching Hospital (NTUVH) from January 2014 through December 2015. Of the 60 dogs recruited, 20 (33.3%) had concurrent disease and 40 (66.7%) had only B. gibsoni infection. The severity of anemia in B. gibsoni infected dogs with concurrent or without concurrent infection was not significantly different. The most commonly observed hematological abnormalities were anemia (49/60, 81.7%) and thrombocytopenia (37/60, 61.7%). Of 49 dogs, 24 (49%) had severe to very severe anemia (PCV < 20%). The main biochemical abnormalities included hyperglobulinemia (28/53, 52.8%), hyperbilirubinemia (10/28, 35.7%) and elevated hepatic enzyme activity (7/48, 14.6%). In addition, 2 of the 60 the client-owned dogs and 5 of the 33 B. gibsoni-positive stray dogs were detected as having a naturally atovaquone-resistant strain, using the SimpleProbe® assay. The study results provide a useful clinical presentation of B. gibsoni infection and raise the issue of the naturally atovaquone-resistant strain currently existing in Taiwan.