Canine babesiosis in Europe is generally caused by Babesia canis canis and Babesia canis rossi. Here we describe the first two autochthonous cases of Babesia gibsoni (Asian genotype) infection in Germany. Two American pit bull terriers showed clinical and hematologic signs consistent with babesiosis. Polymerase chain reaction (PCR) analysis of the 18S rDNA of blood samples revealed 486 bp fragments. The sequences were 100% identical to each other and 100% identical to Babesia gibsoni (Asian genotype). These results represent the first genetic evidence of Babesia gibsoni (Asian genotype) parasites in dogs in Western Europe.