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This paper is the result of a collaboration between the Institute of Research and agri-food Technology (IRTA) in Spain and INRAE GAFL. It follows on from joint works on the sequencing of the Texas Almond genome and the development of an Axiom 60K SNP Array for almond. INRAE GAFL and IRTA maintained in their collections more 250 almond accessions from different origins. We performed a genetic structure analysis of this germplasm and highlighted the existence of 5 ancestral groups races. One of them was formed exclusively by Spanish accessions, while the rest were formed mainly by accessions from China, Italy, France and the USA. We also detected a strong genetic relatedness between accessions from France and the USA. Our genetic results agree with the archaeological and historical evidences that separate the modern almond dissemination into four phases: Asiatic, Mediterranean, Californian and southern hemisphere. In the second part of this study we performed a Genome-Wide Association Study (GWAS) which, in addition to additive effects, also took account of the non-additive effects, as dominant-recessive or overdominant interactions. The traits under study were the nut and kernel weight, the crack-out and double kernel percentages, the blooming time. Through a candidate gene analysis, we were able to propose one candidate gene responsible of the main QTL found in crack-out percentage, 2 candidate genes for the two QTLs found in double kernels percentage et one candidate gene for the QTL found in Blooming time. Our study enhances our knowledge of almond dissemination history and will be very useful on almond breeding.