We investigated the source of fungi in the lungs of patients with hematological malignancies who had invasive pulmonary fungal infections (IPFI). We also conducted a prospective study to evaluate the efficacy of different mouthwash solutions in preventing IPFI in patients with hematologic malignancies. In order to determine the source of fungi in the lungs of 30 patients with hematologic malignancies who had IPFI, we collected samples from sites with suspected fungal infection and used PCR and sequencing for pathogen identification. For the prospective study, we enrolled 158 patients with hematological malignancies who had IPFI and randomly assigned them to one of three mouthwash groups: 1% nystatin, 2.5% sodium bicarbonate, or normal saline. Fungal staining and incidence of IPFI, oral fungal infection, and intestinal fungal infection were evaluated. We showed that 96.7% of the fungi isolated from the throats and the lungs were identical; 76.9% of the fungi from the lungs and digestive tracts were identical and, 84.6 % of the fungi from the throats and digestive tract were identical. Patients using 1% nystatin had lower incidence of IPFI (1.6%) and fungal enteritis (1.6%) than those using sodium bicarbonate (16.3% and 14.3%) or normal saline (27.7% and 12.8%). All treatments had low incidences of oral fungal infections (0 to 4.3%). Our data showed that fungi originating from mouth and throat cause IPFI. We also showed that use of a prophylactic mouthwash containing 1% nystatin was effective in preventing IPFI in patients with hematological malignancies.