Merino sheep breed is the most important breed in Spain according to their census. It is the most censed meat production sheep breed in Spain. It has played an important role in the politic, biologic, economical and livestock aspects. The aim of this study is assess the situation of the most important traditional strains in Spain of Merino breed ("Serena", "Higalgo", "Granda" y "López-Montenegro") using genealogical and molecular information. The most influential strains in the present Merino population are "Serena" and "Hidalgo" (27% and 15% respectively). "Lopez-Montenegro" and "Granda" strains have only 0.3% of influence. The breeder's preferences in raise some strains have been evidenced. This task could endanger the intra population genetic variability of the Merino breed and some traditional strains could disappear because of their economical worse morphological and productive trait. The two more influential strains ("Serena" and "Hidalgo") have shown the lowest value of the molecular variability parameters. However the highest values have been shown by "Granda" and "López-Montenego" strains (observed heterozygosis (Ho) = 0.67 and 0.70; expected heterozygosis (He) = 0,68 and 0,72; and average number of alleles per locus was 7,45 and 7,97 respectively). We found that the coefficient of genetic differentiation value (FST) using genealogical information, for the four strains analyzed, was 30% higher than using molecular information.