In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using model-based and distance-based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classified into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best-supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection.