Chilean sheep breeds have a significant founder effect since they descend from very few parents, in some cases population inbreeding has increased and in others there have been significant differentiation processes as compared to their original population. The objective of this study was to estimate the current status of genetic diversity in sheep herds, which comprise the main sheep breeds in Chile, using molecular methods. Animals from four breeding herds were sampled and analyzed. The breeds studied were Corriedale, Suffolk Down, Romney Marsh and Chilota, these are the predominant numerical pure breeds in Chile. From each breed population 40 animals were sampled. Genetic characterization was done using nine microsatellite molecular markers (SSR) recommended by FAO-ISAG. Results showed that in the Chilean sheep herds there are low genetic complementarities among breeds and a high risk of losing genetic diversity due to inbreeding in Chilota and Romney Marsh breeds.