Analyses of genetic diversity and phylogenetic relationships illuminate the origin and domestication of crop species and have important implications for plant breeding programs and the conservation of genetic resources. Apricot (Prunus armeniaca L.) genetic resources in collections that are widely dispersed around the world were assessed using 25 simple sequence repeat (SSR) markers. Analysis of allelic diversity among SSR data revealed at least a double pattern of diffusion from Central Asia to eastern and western countries with a clear east-west loss of genetic diversity related to the genetic bottleneck during apricot domestication. Structure and phylogenetic analysis indicated that accessions from Central Asia and China were genetically most diverse, suggesting that this large region constitutes the apricot center of origin.