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A comparison between a rare old breed and a common breed of ovine prion protein (PrP) genotype profiles was performed in 3 Romanian sheep flocks. The total number of animals used in the research was 698 sheep, of which 53 were Merino breed (MB) rams, 12 were Tigaie with Black Head breed (TBHB) rams, 340 were MB ewes, and 293 were TBHB ewes. The PrP genotype was investigated by identification of codons 136, 154, and 171 and by gene sequencing between codons 101 and 227. All sheep groups contained the ARR, AHQ, ARH, ARQ, and VRQ haplotypes, with frequencies ranging from 1.37% (ARH in TBHB ewes) to 51.71% (ARQ in TBHB ewes). TBHB had a low prevalence of AHQ (2.05% in ewes, 4.17% in rams), ARH (1.37% in ewes, 4.17% in rams), and VRQ (1.88% in ewes, 8.33% in rams). The highest haplotype in TBHB was ARQ (51.71% in ewes, 37.50% in rams). ARQ was the most frequent haplotype in the MB (49.41% in ewes, 42.45% in rams). MB had a low prevalence of AHQ (3.24% in ewes, 6.60% in rams), ARH (1.47% in ewes, 5.66% in rams), and VRQ (3.53% in ewes, 9.43% in rams). The results indicated that 66.66% of TBHB rams and 68.26% of TBHB ewes have scrapie-resistant genotypes, despite the absence of a genetic selection program for scrapie. The proportion of scrapie resistant alleles was higher in the TBHB rams than in the MB rams.