The aim of the present study was to detect and characterise the species and subspecies of Babesia spp. that cause canine babesiosis in Croatia. Twenty-eight dogs with typical signs of babesiosis (lethargy, anorexia, fever, dark urine and thrombocytopenia) were included in this study. Their blood smears showed the presence of Babesia canis . The results showed the detection of one subspecies, namely Babesia canis canis using PCR, and subsequent sequence analysis demonstrated portions of the nss rRNA gene in 27 out of 28 samples. Sequence analysis of the isolates showed 100% identity in 11 samples, 99.7% identity (one nucleotide difference) in 11 samples and 99.4% identity (two nucleotides difference) in 5 samples with B. canis canis . The results of this study confirm the presence of B. canis canis in infected dogs in Croatia and demonstrate a slightly new genetic variant of Babesia subspecies.