Canine babesiosis in Hungary has always been a severe and frequent disease, attributed to infection with Babesia canis transmitted by Dermacentor reticulatus. Identification of the disease agent has been based merely on size and morphology of the intraerythrocytic parasites and no evidence has been found concerning the subspecies (genotype) of B. canis. Therefore, a molecular survey on natural Babesia infection of dogs in Hungary using PCR and sequence analysis was attempted to clarify the subspecies (genotype) and to obtain information on the occurrence of B. canis. A total of 44 blood samples from dogs showing clinical signs of babesiosis were collected. A piroplasm-specific PCR amplifying the partial 18S rRNA gene yielded an approximately 450 bp PCR product in 39 (88.6%) samples. Thirteen positive samples originated from Budapest and 26 from 21 other locations. Five PCR products were chosen randomly for sequencing. The partial 18S rDNA sequences were submitted to GenBank (accession numbers AY611729; AY611730; AY611731; AY611732 and AY611733). The sequences showed 100% homology to one another or differed by one nucleotide. BLAST search against GenBank revealed the highest similarity (99.8 or 100%) with Babesia canis canis. The implication of these data, for the further study and diagnosis of canine babesiosis is discussed.