(1) Background: Emerging fungal infections associated with spp. and (S/L) are becoming more frequent and are very difficult to treat. Our objective was to analyze the frequency and management of S/L isolates in lung transplant (LTx) recipients, the patient outcomes and in vitro antifungal sensitivity. (2) Methods: We included all patients with S/L isolation during post-transplant follow-up. Data were collected from electronic medical records. All samples were cultivated on Sabouraud Chloramphenicol agar. Isolations of S/L were submitted to in vitro susceptibility tests. (3) Results: A total of 11 (2%) of the 576 LTx recipients included had at least one isolation of S/L. Classification for the 11 cases were colonization (4; 36%) and infection (7; 65%). Five infections were pulmonary (71%) and two were disseminated (29%). complex was the most frequently occurring isolation in patients with pulmonary disease while was the most frequent in patients with disseminated disease. Ten patients were treated. The most frequent antifungal drugs used were voriconazole (n = 8) and terbinafine (n = 6). Seven patients (70%) received more than one drug. The mortality rate associated with isolation was 50% for colonization and 100% for disseminated disease. (4) Conclusions: spp. and infections are associated with high morbidity and mortality rates. New diagnostic and therapeutic tools are required to reduce the impact of these infections.