Babesia gibsoni is a morphologically small Babesia species that infects dogs. Molecular techniques have shown that some small Babesia sp. recently described in canids are not related to the original B. gibsoni and they should be assigned to separate taxons. Although the 18s rRNA gene of true B. gibsoni isolates has been studied in the USA, Asia and Australia, no molecular data on the presence and genetic characteristics of B. gibsoni in Europe are available. Blood collected from a Babesia-symptomatic dog from Spain was used for DNA diagnosis by seminested PCR. DNA amplification was positive and the complete 18s rRNA gene of the dog isolate was sequenced, showing 98% homology with B. gibsoni (isolate Asia 1). Evidence from phylogenetic analysis indicated that: The Spanish isolate unambiguously belongs to the B. gibsoni group. The B. gibsoni complex might be diphyletic. In the absence of genetic data from African isolates of B. gibsoni, Asia seems to be the most likely geographical location of origin.