Aim of study: To validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, and develop a cost effective genotyping system to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment.Area of study: SpainMaterial and methods: Nine sheep breeds were sampled: Rasa Aragonesa (n=38), Navarra (n=39), Ansotana (n=41), Xisqueta (n=41), Churra Tensina (n=38), Maellana (39), Roya Bilbilitana (n=24), Ojinegra (n=36) and Cartera (n=39), and these animals were genotyped with the Illumina OvineSNP50 BeadChip array. Genotypes were extracted from the sets of 249 SNPs and 163 SNPs for parentage assignment designed in France and North America, respectively. Validation of a selected cost-effective genotyping panel of 158 SNPs from the French panel were performed by Kompetitive allele specific PCR (KASP). Additionally, some functional SNPs (n=15) were also genotyped.Main results: The set of 249 SNPs for parentage assignment showed better diversity, probability of identity, and exclusion probabilities than the set of 163 SNPs. The average minor allele frequency for the set of 249, 163 and 158 SNPs were 0.41 + 0.01, 0.39 + 0.01 and 0.42 + 0.01, respectively. The parentage assignment rate was highly dependent to the percentage of putative sires genotyped.Research highlights: The described method is a cost-effective genotyping system combining the genotyping of SNPs for the parentage assignment with some functional SNPs, which was successfully used in some Spanish meat sheep breeds.