Soybean [Glycine max (L.) Merr.] was domesticated in China, and cultivated landraces were initially distributed throughout Asia and more recently extended to Europe and America. Previous studies of genetic diversity suggest a strong genetic bottleneck between Asian and North American soybean genetic pools. However, little is known about the potentially useful genetic diversity present in European soybean germplasm. We evaluated genetic diversity by phenotypic characterization and by comparing nuclear and cytoplasmic microsatellites in 301 genotypes of an INRA soybean collection with those of 31 European breeding lines and 17 ancestors from American cultivars (representing 83% of the North America diversity). We showed that the INRA collection contains 14 and 8% more diversity than the European breeding lines and American ancestors, respectively, based on Nei diversity (He). The genetic structure of this INRA collection does not correlate with either geographic origin or phenotypic differentiation. We generated a core collection composed of 50 accessions from the INRA collection and European breeding lines. This core collection contains 203 of the 226 microsatellite marker alleles available for this germplasm and is also representative of the diversity of morphological traits in temperate regions (maturity 000 to 111), which will be useful for future breeding programs