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Introduction: Mucormycosis is a fungal infection that can rapidly progress to tissue necrosis and angioinvasion. Diagnosis is classically made by biopsy, which can prove difficult in cytopenic patients. Here we present a challenging case of cerebral angioinvasive mucormycosis (CAM) resulting in complete occlusion of the left internal carotid artery (ICA), a diagnosis made via metagenomic DNA sequencing in a patient that was unable to undergo biopsy. Description: An 18-year-old male with history of aplastic anemia on immunosuppression presented with subacute onset of facial numbness and blurred vision. He was found to have neutropenic fever to 101.1°F and platelet count of 7 x 103/µL. MRA revealed high-grade stenosis of the left ICA with occlusion of the left ophthalmic artery. Sinus involvement was less obvious on MRI, although the left orbit was involved. Extensive infectious, inflammatory, and autoimmune workups were unrevealing. He rapidly developed worsening facial swelling, proptosis, and complete monocular vision loss. MRI and repeat MRA showed new multifocal ischemic strokes with hemorrhagic transformation, midline shift of 2mm, and complete left ICA occlusion. Clinical suspicion for an invasive fungal infection was raised but the patient’s thrombocytopenia precluded diagnostic endoscopic biopsy. Karius testing for next-generation DNA sequencing was sent and returned positive for Rhizomucor pusillus. Despite the initiation of aggressive antifungal therapy, the patient’s condition unfortunately progressed with hydrocephalus, cerebral abscesses, and increasing edema resulting in trans-tentorial herniation. The patient was transitioned to comfort care and succumbed shortly thereafter with his family at the bedside. Discussion: CAM resulting in a complete unilateral occlusion of the ICA is a rare and deadly manifestation of the disease. While typically associated with sinus invasion, cerebral involvement can occur even with limited sinus involvement as noted in our case. The high morbidity and mortality of such cases demand heightened clinical awareness and rapid intervention following early diagnosis. Immunocompromised and cytopenic patients face barriers to diagnosis of CAM due to the invasive nature of standard biopsy; Karius testing provides a meaningful diagnostic alternative.