This lecture was a part of Plant Genetics Seminars - PGS 2017/2018 at Assiut University. These seminars organized by Dr. Ahmed Sallam, Department of Genetics, Faculty of Agriculture, Assiut University Abstract Pomegranate (Punica granatum L.) is one of the oldest known edible fruits. This study was the first time to compare two Punica species, viz., P. protopunica and P. granatum. Three molecular markers, i.e. SRAP, TRAP, and ITAP were used to analyse twelve accessions collected from Egypt, Mexico and Yemen, along with analysis of a gene involved in anthocyanin biosynthesis (pgWD40). All markers revealed the relationship between Punica species and among P. granatum accessions. Sequence analysis of pgWD40 exhibited 98% identity between the two species, supporting earlier reports that P. protopunica could be an ancestral species of P. granatum. The information herein could be used for pomegranate genotyping and breeding programs.