We biochemically analyzed and characterized the genetic structure of a population in danger of extinction, 'Alberes', a local cattle breed of the Catalonian Pyrenees (Spain and France). Ninety-two individuals were analyzed for five polymorphic genetic loci (Hb, Alb, Tf, Gc and Ptf2). The animals were grouped according to coat color: Fagina Alberes variety (N = 39) and Black Alberes variety (N = 53). The genetic structures and relationships between these subpopulations and one 'outgroup' breed ('Bruna dels Pirineus') were analyzed and compared by using F-statistics. We determined that inbreeding in the Alberes breed is not significant, since negative and nonsignificant F(IT) and F(IS) values were obtained. The average genetic differentiation between subpopulations within the Alberes breed was 1.5% (F(ST) = 0.015; P < 0.05), with an effective number of 4.1 individuals exchanged between subpopulations per generation (gene flow). The results obtained in this study corroborate the potential danger of extinction of the breed. The Black Alberes variety is proposed as the principal nucleus of genetic conservation for this breed, as it seems to show a higher degree of genetic isolation from other foreign populations.