Abstract: The development of a simple sequence repeat (SSR) core primer group based on the whole genome sequence of pomegranate and the applications thereof are disclosed. The primer group includes 11 primer pairs: PG080, PG130, PG139, PG152, PG153, PG140, PG098, PG070, PG077, PG090, and PG093. The SSR core primer group of the present disclosure has the advantages such as high polymorphism, good repeatability, stable amplification, and clear and easy to score bands, and is applicable to the fields of pomegranate variety identification, DNA fingerprinting construction, genetic diversity assessment and phylogenetic study, and the like, providing a new tool for pomegranate molecular marker-assisted selection and having an excellent application prospect.