Background and Clinical Significance: Since the prevalence of fungal lung infections is increasing, certain agents, such as Cladosporium spp., have emerged as unexpected causes. Cladosporium spp. fungi are ubiquitous in environments such as soil, fruits, and wine corks; they are a part of the normal human skin flora; and they are known respiratory allergens. Case Presentation: A patient with a history of post-COVID-19 syndrome and AIDS presented with lung pathology indicative of an invasive fungal infection. The initial histopathological examination revealed numerous yeast-like cells with narrow-based budding, which led to a mistaken diagnosis of cryptococcosis. However, further detailed examination revealed sparse hyphae in the lung tissue, suggesting a more complex fungal infection. Molecular analyses and sequence BLAST alignment were performed, ultimately identifying the infectious agent as "Cladosporium species novum", a rare cause of invasive pulmonary cladosporiasis. Conclusions: Invasive pulmonary cladosporiasis is a rare condition, and the morphological features of the fungus alone were insufficient to establish a correct diagnosis. A comprehensive pathohistological and molecular approach with bioinformatics tools is essential for the correct identification of rare and potentially life-threatening fungal pathogens in immunocompromised patients.