Traditionally, breeding programs have estimated and managed inbreeding based on pedigree information. The availability of genomic marker panels has made possible new alternatives to achieve more precise estimates, for example in case of missing pedigree. The objective of the present study was to assess and compare, different estimation methods (pedigree-based methodologies, single SNP-based approach (homozygosity) and runs of homozygosity-based method) to analyze the evolution of genetic diversity measured as inbreeding or as coancestry of 3 selected populations of Latxa dairy sheep (Latxa Cara Rubia and Latxa Cara Negra from Euskadi and Navarre). Genomic data came from 972 artificial insemination rams genotyped with the Illu-mina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) whose genealogy consisted of 4,484 animals. Inbreeding estimates based on molecular data were more similar between them than compared with those based on pedigree information. However, the SNP-based approach estimations of effective population size differed more, reflecting the sensitivity of effective population size to small changes in the evolution of inbreeding. The 2 Latxa Cara Negra populations showed increases of inbreeding rates with time and effective population sizes between 64 and 103 animals, depending on breed and methodology used. The Latxa Cara Rubia population did not show an increase in inbreeding rate, mainly due to semen importation from the related French population of Manech Tête Rousse. The effective size estimates based on coancestry increase show a higher variability and they are more sensitive to the source of information and the data structure considered. Realized effective population size based on individual increase in inbreeding were in agreement with the previous estimates. Coancestry evolution analysis based on DNA information showed an increase on coancestry during the last 10 yr in all breeds, as a consequence of the selection process. Moreover, the increase on coancestry between Latxa Cara Rubia and Manech Tête Rousse was more noticeable between than within each of those breeds.