Secondary burials and the use of cave or rock-shelter as cemeteries is one of the major characteristics of mortuary practices in East Indonesia, especially after the early Metal age. However, detailed anthropological analysis and reports of these remains are still very limited in East Indonesia. In this presentation, I report on the detailed anthropological studies of excavated Early Metal aged burial remains from Aru Manara rock-shelter site in Northern Maluku and Topogaro cave complex site in Central Sulawesi. This is followed by a discussion focussing on similarities in burial tradition and locality of the two sites, as well as relationships with burial practices across Eastern Indonesia, and Island environments more generally.