Stem-end rot (SER) is a major post-harvest disease that significantly reduces the quality and shelf life of mangoes, particularly under the tropical condition. This study aimed to identify the causal agents associated with SER in Bangladesh through morphological and molecular characterization and to evaluate eco-friendly management strategies based on botanical extracts. Samples including dried branches, dead twigs, dried panicles and mummified fruits were collected from major mango-growing regions e.g. Rajshahi, Chapainawabganj, Rangpur and Natore districts. Six fugal isolates were obtained and initially identified as Lasiodiplodia spp. based on colony morphology and conidial characteristics. Molecular characterization using ITS region sequencing confirmed the presence of two distinct species: Lasiodiplodia theobromae and Lasiodiplodia viticola, the second being first recorded for Stem-end rot in Bangladesh. Physiological studies revealed that the isolates exhibited optimal growth at 25oC and pH 6.0, with significant thermotolerance observed in certain strains. Pathogenicity tests confirmed that all isolates were highly virulent, capable of penetrating non-wounded host tissues, with the highest disease severity (81.25%) observed in Lengra variety. In vitro screening of 14 botanical extracts was conducted against Lasiodiplodia isolates. Among the treatments, Garlic (Allium sativum) and Alamanda  (Allamanda cathartica) extracts emerged as the most potent, achieving complete (100%) mycelium inhibition. In vivo assays further demonstration that Garlic and Alamanda extracts significantly suppressed disease progression and reduced the infection area to 1.25% and 5.75% compared to 95.50% in the control. These results suggest that A. sativum and A. cathartica extracts are highly effective and sustainable altranatives to synthetic fungicides for managing stem-end rot in mango