© 2022 International Society for Horticultural Science. All rights reserved.Pomegranates are widely spread and consumed throughout the world. Pomegranates are fruits with high antioxidant content and high anti-tumor and anticancer activities because of their precious secondary metabolites. The use of pomegranates in many fields has increased the demand for pomegranate fruit. This has led to an increase in pomegranate production. To obtain new cultivars of fruit trees, novel plant breeding methods are being developed to overcome traditional breeding limits. Until recently, the targets of genetic improvement of pomegranates primarily improved fruit yield, juice content and maturity. The latest developments in genomic analysis technologies have opened new horizons for increasing the efficiency of plant breeding. New genomic-based approaches such as genome-wide association studies (GWAS) and genomic selection (GS) for plant breeding and molecular genetics research are particularly useful in breeding perennial plants such as pomegranates. This review describes the potential of molecular and genomic assisted breeding using novel genomics-based approaches to achieve results in less time than conventional pomegranate breeding. First, it includes all molecular markers and genome sequence studies available in pomegranate breeding. Next, we introduce quantitative trait locus (QTL) mapping, GWAS, and GS studies on pomegranates. We also review novel technologies for rapid generation progress. Finally, we discuss the prospects for genomics-assisted pomegranate breeding as well as the issues that must be addressed during the breeding process.