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Mango stem end rot (SER) is a significant post-harvest disease affecting mango production globally, particularly in tropical, subtropical, and arid regions. It ranks as the second most severe mango disease after anthracnose, causing substantial yield losses, quality deterioration, and reduced market value. The disease is caused by a complex of fungal pathogens, predominantly Lasiodiplodia theobromae, along with species from the Botryosphaeriaceae family, such as Dothiorella spp., Neofusicoccum spp., Phomopsis mangiferae, and Pestalotiopsis spp. The infection process begins at flowering, with pathogens remaining quiescent until post-harvest, where conducive conditions trigger symptom development. Molecular diagnostic techniques, such as species-specific primers and PCR assays have advanced pathogen identification and enabling targeted management strategies. Unlike previous studies focusing on specific regions, this review provides a comprehensive global perspective on SER, covering its history, economic impact, epidemiology, disease cycle, pathogen identification, host range and control measures. Additionally, it explores the role of molecular techniques in improving disease diagnosis and management, offering insights for mitigating the spread of SER in mango-producing regions.