Fungi often infect mammalian hosts via the respiratory route, but traumatic transcutaneous implantation is also an important source of infections. Environmental exposure to spores of pathogenic fungi can result in subclinical and unrecognised syndromes, allergic manifestations, and even overt disease. After traumatic cutaneous inoculation, several fungi can cause neglected mycoses such as sporotrichosis, chromoblastomycosis, mycetoma, entomophthoramycosis, and lacaziosis. Most of these diseases have a subacute to chronic course and they can become recalcitrant to therapy and lead to physical disabilities, including inability to work, physical deformities, and amputations. For many years, paracoccidioidomycosis was considered the most prevalent endemic systemic mycosis in the Americas, but this situation might be changing with recognition of the worldwide presence of Histoplasma capsulatum. Both paracoccidioidomycosis and histoplasmosis can mimic several infectious and non-infectious medical conditions and lead to death if not recognised early and treated. Cutaneous implantation and systemic mycoses are neglected diseases that affect millions of individuals worldwide, especially in low-income countries where their management is suboptimum because challenges in diagnosis and therapeutic options are substantial issues.