Seven healthy sheep and 10 sheep diagnosed with piroplasmosis based on clinical signs were tested for the presence of babesiae and theileriae. Using the molecular techniques, two species of theileriae were detected and characterized. Theileria ovis was present mostly in healthy sheep and in Rhipicephalus ticks collected from infected sheep. Theileria sp. OT3 parasite was detected mostly in ill animals which represent additional evidence to the possible pathogenic nature of Theileria sp. OT3. The presence of babesiae in sheep or in ticks was not determined. The results of this study showed that ovine piroplasmosis due to Theileria is present in Southern Croatia. It was concluded that clinical diagnosis of ovine piroplasmosis should be confirmed by molecular analysis in order to identify the species of piroplasm, to select the appropriate treatment and to exclude the threat for public health.