Mango, the “King of Fruits, is an economically significant fruit in the world, but the king of fruits is also facing numerous challenges due to a perennially shifting climate and developing biotic stresses under different agroecologies. Future climate predictions indicated a considerable increase in climatic patterns for climate extreme predictions. The world’s minimum temperature is expected to climb by 2.8 degrees Celsius by mid-century (2040–2070). To address the negative effects of climate change scenarios, climate-smart technology for diagnosing and detecting plant diseases is required. For quantifying detrimental climate impacts on mango plant diseases, early detection of plant infections is an acceptable preventive technique for mango yield and quality control. As a result, effective diagnostic approaches and instruments that are simple, specific, fast, and economical have to be produced. This chapter provides a complete overview of the current plant pathogen diagnosis methodologies. Furthermore, it focuses on current advancements in the subject, beginning with an appreciation of fundamental research. Through a synthesis of recent findings, it illustrates the current fungal phylogenetic landscape and recommends important areas for future research. Fingerprinting techniques and next-generation sequencing approaches are thoroughly examined, showing their practicality and limitations in determining genetic diversity among fungal isolates. Furthermore, multi-omics methods, including genomics, transcriptomics, and proteomics, are investigated to provide insight into fungal pathogenesis and host interactions. The use of machine learning and artificial intelligence for data analysis is being investigated as a viable way to streamline research processes and improve the accessibility of results. Finally, the need for collaborating as researchers, and bioinformaticians to advance fungal phylogenetics and improve disease management approaches. This chapter aims to add to the most recent diagnostic techniques for plant fungal disease, such as fungal phylogenetics, and to motivate future research efforts in the field.