Domestic chestnut is one of the most widespread tree species in south Switzerland. It covers more than 26.000 ha. In the past, chestnut fruits used to be of vital importance in the diet of people and livestock. Three different kinds of molecular markers: Random Amplified Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphism DNAs (AFLPs) and Inter Simple Sequence Repeats (ISSRs) have been used for studying the genetic variability in 52 Swiss accessions of cultivated and wild Chestnut (Castanea sativa Mill.). Variability within and between cultivars is examined. 98 RAPD, 222 AFLP and 35 ISSR polymorphic markers were amplified using 12, 4 and 5 primers respectively. Clustering analysis performed with the three sets of markers group the 52 studied accessions according to their similarity coefficients separated the genotypes into clear groups with some differences. It is interesting to note that AFLP generated the highest number of polymorphic bands and clustered fairly chestnut cultivars. These results allowed us to resolve problems generated by synonyms and homonyms in different chestnut accessions. Molecular markers results are comparable. The similarity matrices based on the three sets of data give a high significant correlation between RAPD and AFLP, RAPD and ISSR data (r = 0.78 and r = 0.75 respectively).