Juglans is an economically important genus distributed all over the world. Due to its high value, there is a large interest in genetic markers for population genetic analyses and the certification of reproductive material. Using chloroplast genomes of different Juglans species, we developed a highly polymorphic and reliable chloroplast SSR marker set of eleven cpSSRs. It was successfully tested in five different Juglans species. Genetic differentiation among species and provenances within species was assessed. We were able to define a total of nine different chloroplast haplotypes using the novel cpSSR markers with up to four different haplotypes within a single Juglans species. Due to the cost and labor effective character of SSR markers, when compared to other available methods, such as whole chloroplast genome sequencing or SNP analyses, this novel cpSSR marker set will contribute to future population genetic studies in the Juglans genus.
