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In this study, the frequency of Theileria and Babesia species in sheep and goats was assessed via reverse line blotting (RLB). A total of 263 apparently healthy sheep and goats, from 16 randomly selected flocks located in 9 localities situated in 3 bioclimatic zones in Tunisia, were investigated for the blood protozoans. RLB hybridization with polymerase chain reaction detected only Theileria ovis in sheep and goats, accounting for 22.4% (95% confidence interval [CI]: 17.6-27.1%) positive samples. The infection rate in sheep (28.1%; 95% CI: 23.8-32.3%) was higher than in goats (4.7%; 95% CI: -10.9 to 20.4%). Neither Babesia nor mixed infections were detected. Only two Ixodid tick species (Rhipicephalus turanicus and Rhipicephalus bursa) were collected from the examined sheep and goats in 5 localities. R. turanicus was the dominant species (95.5%) collected mainly in the humid zone, while apparently rare in the sub-humid zone. R. bursa was the only species collected in the semi-arid area. RLB analysis identified six different piroplasms in ticks, with an overall prevalence of 31.5% (95% CI: 28.1-34.9%). Twenty percent (95% CI: 14.4-25.5%) of the collected ticks tested positive for Theileria spp., 3% (95% CI: -5.6 to 11.6%) for Babesia spp. and 0.9% (95% CI: -8.1 to 9.9%) of the ticks harbored both genera; several of these species are not known to occur in small ruminants. This is the first report on the detection of Theileria and Babesia species DNA in small ruminants and ticks in Tunisia. (C) 2013 Elsevier B.V. All rights reserved.