Endophytes are a unique group of microorganisms that reside within plant tissues without causing any apparent harm to their host. The present review focuses on various aspects of endophytic research conducted in the Kingdom of Saudi Arabia over the past decade. It highlights the diversity of endophytes isolated from native and medicinal plants adapted to arid and semi-arid environments. Furthermore, this review provides a comparative analysis of different methodologies used for the identification of endophytes, emphasizing the transition from traditional techniques to modern molecular approaches. Advanced tools such as DNA barcoding, Random Amplified Polymorphic DNA (RAPD) analysis and sequence-based identification using BLAST have been increasingly applied in recent years for accurate characterization of endophytes. A compilation of commonly reported endophytic species isolated from various plant hosts across different regions of Saudi Arabia is also presented. The rich floral diversity of the region, including desert-adapted and medicinal plants, represents a valuable source of bioactive compounds as well as endophytic microorganisms with significant biotechnological potential. Given the unique ecological conditions of Saudi Arabia, further exploration and identification of endophytes from indigenous plant species are of great importance. Such studies may contribute to advancements in pharmaceuticals, agriculture and environmental sustainability, ultimately benefiting human health and scientific development.