Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete features within the Dinaledi Chamber and the Hill Antechamber. These are the most ancient interments yet recorded in the hominin record, earlier than evidence of Homo sapiens interments by at least 100,000 years. These interments along with other evidence suggest that diverse mortuary practices may have been conducted by H. naledi within the cave system. These discoveries show that mortuary practices were not limited to H. sapiens or other hominins with large brain sizes.