D. Geneti and D. Merga Arabica coffee, Disease resistance, Improvement, Marker-assisted selection, QTLs 17-48 9 (2) April 2025 Improving coffee through conventional breeding programs is challenging due to its perennial nature, the high cost of field trials, and dependence on environmental conditions. These factors have prompted researchers to apply marker-assisted selection (MAS) studies to further exploit the genetic diversity of Arabica coffee and improvement for desirable traits. This review summarizes the available information on the application of MAS in Arabica coffee and identifies the challenges and opportunities for future research to address issues related to its application. Research on the phylogenetic origin and evolution of Arabica coffee using various MAS techniques has shown Coffea species clustering based on their botanical types, geographical origins, and maternal progenitors, with a specific focus on Ethiopian-origin Arabica coffee. Studies on genetic diversity using MAS have demonstrated that Arabica coffee germplasm in Ethiopia has a broad genetic base, making it valuable for developing varieties capable of sustaining global coffee production. Arabica coffee germplasm gene bank were assessed using MAS, identifying 2,533 genotypes for core collections to assist breeders in selecting parent plants and reducing maintenance costs. Research on linkage and QTL mapping through MAS has identified mapping strategies for various desired traits, although progress in this area is still in its infancy, with limited success. Different candidate genes have been identified for major coffee diseases such as coffee berry dissease (T, R, K, and ckl-1 genes), coffee leaf rust (SH1–SH9), and coffee wilt disease (strains affecting only Arabica coffee). Furthermore, biochemical candidate genes have been identified for key compounds like caffeine (Caffeine-5), sucrose (Sucrose-3), trigonelline (Trigonelline-1), fatty acids (Fatty acid-1), and CGAs (CGAs-1). However, significant challenges remain in overcoming the limitations of MAS research on Arabica coffee, particularly in Ethiopia, where the highest diversity of Arabica coffee is recorded. To advance MAS applications in Arabica coffee research, particularly in developing countries like Ethiopia, adequate policies must be implemented to encourage innovation and investment in this field.