This article aims at presenting genetic analysis of Babesia canis protozoans that were isolated from dogs in last years. Canine babesiosis is a severe disease characterized by fever and intravascular hemolysis manifested by a syndrome of anemia, hemoglobinuria and jaundice. The etiological agent is are protozoan from the family Babesiidae, transmitted by blood-sucking ticks. Molecular biology techniques have shown that the genetics of these parasites is extremely diverse. DNA analysis of Babesia canis strains isolated from dogs revealed increased frequency of new variants of these protozoa over the past years. Some of these variants are highly virulent and present also significant resistance to drugs that are commonly used for treating babesiosis in dogs.