Babesiosis is common infectious agents of haemolytic anaemia in dogs in Croatia. Based on morphology of merozoites, Babesia/Theilera species are divided on big and small piroplasms. Differentiation between big of small piroplasms is not possible in the tissue imprints, unlike in peripheral blood smear, because they change their morphologic characteristic. The use of molecular methods for genetic typing of causative agent of haemolytic anaemia in dogs is necessary because morphologically is not possible to distinguish species, or subspecies of piroplasms. This is generally done from the fresh blood samples, but sometimes is necessary to perform genetic typing from the blood smear, or post-mortem tissue imprints. In this study genetic typing is performed from 22 grinds of cytological samples using three different protocols. Previously, cellularity, merozoites finding and their morphology have been analysed in all samples by microscopic method. Using different PCR protocols DNA is duplicated in 12 samples from 13 cytological positive samples. Genetic typing is performed on 9 samples successfully duplicated in third protocol. DNA of Babesiosis is duplicated using three different protocols: (I) simple PCR reaction (II) double PCR reaction „nested“ (III) simple PCR reaction from purified and concentrated DNA samples. The successfulness of DNA multiplication was different and amounted 31%, 70% and 70%. Significant differences are established in successfulness of multiplication between tissue imprints and blood smear using the same protocol. Using the second protocol successfulness of multiplication in blood smear samples was 60%, and from tissue imprints 75%. In third protocol successfulness of multiplication in blood smears samples was 40% and in tissue imprints samples 88%. The difference in the successfulness of duplication points on necessity of using different molecular protocols for detection of piroplasms in the tissue imprints and blood smear. The successfulness is confirmed with analysis of nucleotide sequences and detection of protozoon B. canis canis. In this study suitability of genetic typing and analysis of nucleotide sequences of pathogens is detected. The analysis of nucleotide sequences is suitable for detection of species/ subspecies of piroplasms from archival cytological samples stained by Giemsa or Diff Quick®.