Traditionally, inbreeding estimates have been estimated based on pedigree information. However, in sheep there is a considerable proportion of unknown pedigree due to natural mating and lack of filiation analysis. Therefore, there could be an under estimation of inbreeding coefficients based on pedigree. In the genomics era, genomic information can be used to estimate inbreeding. In this study, three different inbreeding estimation methods were assessed (a pedigree-based methodology, a single SNP-based approach and a ROH based method) to analyse the genetic diversity of two populations of Latxa Cara Negra breed: Latxa Cara Negra from Euskadi (LCNEUS) and from Navarre (LCNNAF). A total of 533 animals were genotyped with the Illumina OvineSNP50 BeadChip, bringing around 41700 SNPs and 2505 animals in pedigree. The results showed an effective population size below 100 in most of the evaluated cases. In addition, LCNEUS showed a higher genetic diversity than LCNNAF for each evaluated method. These results suggest that it could be interesting to consider these estimates in the management of both populations.