Canine babesiosis constitutes a major global veterinary medical problem caused by tick-borne hemoparasites Babesia gibsoni and Babesia canis. Babesia gibsoni induces more severe clinical signs and is mainly transmitted by the ixodid Haemaphysalis longicornis. In Japan, B. gibsoni is primarily found in the western districts, with few records in the eastern parts. The aim of the current investigation was to evaluate distribution patterns of B. gibsoni infection in 9 Japanese islands and peninsulas using direct microscopy and PCR. Therefore, 196 hunting dogs were randomly sampled during the period from March to September 2011. Ages and sexes of dogs were identified. Direct microscopy of Giemsa-stained blood smear revealed pear-shaped piroplasms of B. gibsoni in 3 (1.6%) dogs. PCR was done initially with the universal primer set (B18S-F and B18S-R) amplifying the 1,665-bp portion of the 18S rRNA gene, followed by the specific primer set (Bg18F1 and Bg18R2) amplifying 2,363-bp fragments of the same gene. Accordingly, 84 (42.9%) and 8 (4.1%) dogs were positive, respectively. The current investigation shows that canine babesiosis was recorded in all islands except for Sado Island, Atsumi Peninsula, and Tanegashima Island. The highest infection rate was detected in the main island of Okinawa, while the lowest was on Ishigaki Island. Both sexes were non-significantly infected. However, the diversity of infection in islands was significantly different (P < 0.05). Although B. gibsoni has been previously found in western and eastern Japan, the present work highlights the prevalence of infection in many Japanese districts, including islands and peninsulas, giving realistic data that can facilitate treatment and control.