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There is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long-term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty-one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour-joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between-breed variation ranged from -12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within-breed diversity the removal of a breed could also produce an increase in diversity (-0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations.