A 65-year-old male patient, who was a farmer from Hebei, went to the local hospital for “intermittent fever of unknown origin” on August 12, 2021, and his blood test showed pancytopenia, which was misdiagnosed as a blood system disease, after antibiotic treatment, ferrous succinate supplementation for restoring hematopoietic deficiencies. The symptoms were improved temporarily, but his condition recurred, and the patient was hospitalised for more than 6 months. On February 19, 2022, he developed a fever again, with a body temperature of up to 39 °C, and was admitted to Hebei Provincial People’s Hospital for further diagnosis and treatment. The patient has a history of previous contact with street dogs. The history of blood-sucking sandfly bites exposure is unknown. The admission examination showed anemia appearance, soft abdomen, liver and spleen slightly hard. Blood count showed that the white blood cell count was 0.72 × 10⁹/L, the neutrophils count was 0.34 × 10⁹/L, the lymphocytes count was 0.30 × 10⁹/L, the red blood cell count was 3.03 × 10¹²/L, the hemoglobin level was 72 g/L, the platelet count was 46.00 × 10⁹/L. Immunological tests showed that immunoglobulin G level was 32.9 g/L, complement C3 was 0.53 g/L, complement C4 was 0.095 g/L, complement C1q was 144.6 mg/L, direct anti-human globulin was positive for IgG and positive for antinuclear antibodies. Relevant pathogens were tested. The fungus D-dextran was 814.0 pg/ml, human herpesvirus type 4 (HHV-4) PCR was below 500 copies/ml. The chest and abdominal CT and ultrasound showed splenomegaly and flaky low-density shadows could be seen in the spleen, with unclear boundaries. Bone marrow aspiration smear showed Leishmania donovalii in and around some macrophages without flagellates. The whole blood samples were sent to Jiangsu Simcere Medical Diagnostics Co., Ltd. for metagenomic second-generation sequencing. A total of 266 335 Leishmania DNA sequences were detected, including 145 767 L. infantiles, 66 243 L. donovalii, 53 461 L. dononii and 28 HHV-4 lesions. Combined with clinical symptoms and laboratory findings, L. donovalii infection diagnosis was made. Intravenous amphotericin B was administrated, starting from 5 mg to 100 mg and gradually ramping up the treatment, the patient’s body temperature decreased after 3 days of treatment, and the body temperature was normal after 1 week. The patient was and then transferred to a specialist hospital for 20 days of continuous treatment before discharged. After about 3 months of follow-up, the patient reported no discomfort and no leishmania on the bone marrow aspiration smear.