A niche in the context of microorganisms defines the specific ecological role or habitat inhabited by microbial species within an ecosystem. For the human commensal Malassezia, the skin surface is considered its primary niche, where it adapts to the skin environment by utilising lipids as its main carbon and energy source. However pathogenic characteristics of Malassezia include the production of allergens, immune modulation and excessive lipid utilisation, which result in several diseases such as pityriasis versicolor, seborrheic dermatitis, Malassezia folliculitis and atopic dermatitis. Recent studies have revealed Malassezia colonisation in internal organs, including the lungs, gut, genitourinary tract, eyes, ears and breast milk. In these organs, Malassezia is associated with diseases linked to respiratory conditions, neurological disorders, gastrointestinal diseases and genital infections. The immune system plays a critical role in shaping Malassezia prevalence, with factors like, immune suppressive drugs and underlying health conditions influencing susceptibility. Accurate diagnosis of Malassezia-related skin disorders is challenging due to its unique growth requirements, but molecular fingerprinting assays and sequencing methods, particularly ITS sequencing, offer precise identification. Treatment involves antifungal drugs, corticosteroids and phytocompounds, yet recurrent infections highlight the need for more targeted therapeutic strategies addressing Malassezia's pathogenic characteristics. Understanding the complex interactions between Malassezia and the host organs is crucial for diagnosis, treatment and prevention and exploring its potentially beneficial roles in health and disease. This review highlights the current findings on the intricate interactions between Malassezia and the diverse ecosystem of the human body, underscoring the complexity of these associations and emphasising their multifaceted role in health and disease.