Pakistan is an agricultural country and its population continues to grow rapidly at an alarming pace. The agricultural sector is playing a vital role in strengthening the economy of the country. Apart from traditional cereals cultivation, climatic conditions of Pakistan are feasible and appropriate for the cultivation of temperate, tropical and subtropical fruits. Thus, diverse environmental conditions allow the farmers to cultivate a variety of fruits which ultimately uplifting the burden from traditionally cultivated crops. In recent years, the cultivation and yield of diferent fruit trees are declining in the country. The key contributors to the decline in fruit crop yield include abiotic stresses, biotic stresses, certain pathogens and nematodes, market devaluation and access, urbanization, poor gardening, poverty climate change, small landholdings, exogenous factors and managerial decisions, etc. So, to counter these fruit yield declining factors the use of advanced molecular markers is a handy option for the improvement of the fruit germplasm in Pakistan. Additionally, they also have diverse applications in the area of genetic diversity, varietal identification studies, hybrid detection, disease diagnostics and sex diferentiation by administering the powerful diagnostic polymorphism detection tools at specific loci and the genome level. This review focuses on exploring the application, recent advancements and future implications of DNA-based molecular markers with the context of their role in the genetic improvement of fruit germplasm that is widely grown in Pakistan like citrus, apples, mangoes, guavas, bananas, date palms and peaches, etc. Furthermore, by ofering a piece of scientific information and addressing developments, notably in DNA-based molecular markers, this review paper may serve as a road map for obtaining high-yielding fruit varieties in Pakistan.