Polyembryonic mango varieties, known for producing multiple seedlings from a single seed, present valuable potential in breeding programs and orchard management. This study examines the response of polyembryonic mango germplasm to the development of symptoms and resistance dynamics against critical soilborne fungal pathogens, including Fusarium spp., Rhizoctonia solani, Lasiodiplodia theobromae, and Ceratocystis fimbriata. A controlled evaluation was conducted to assess disease incidence, symptom progression, and host resistance traits across diverse polyembryonic lines. Findings revealed significant variability in resistance levels, with certain germplasm demonstrating delayed symptom onset, reduced lesion severity, and enhanced plant survival compared to monoembryonic varieties. Resistance mechanisms were associated with increased lignification, phenolic accumulation, and robust root development, which inhibited pathogen invasion and colonization. Notably, polyembryonic rootstocks exhibited superior resilience under pathogen pressure, highlighting their potential as a foundational tool for sustainable mango production. The study emphasizes the strategic importance of polyembryonic germplasm in breeding programs aimed at enhancing resistance to soilborne diseases, including those caused by Ceratocystis, which has emerged as a significant threat. These findings contribute to the development of integrated disease management strategies and climate-resilient mango cultivation systems.