The Halmahera Epaulette Shark is threatened by fishing, habitat loss and degradation, pollution, and climate change. It is taken by artisanal fishing by gleaning (collecting by hand or hand spear on intertidal reef flats at night), extensive gill netting down to 20 m depths, and hand-lining which is prevalent throughout most of its range at 5–15 m depths. There is habitat degradation of reef flats due to dynamite fishing and open-pit mining in coastal zones throughout its range. The mining in the area also poses a threat of heavy metal pollution. A study of mercury in the Halmahera Epaulette Shark shows exposure of 6.50 μg/g creatinine, which is above the safe threshold of 1 μg/g creatinine (Jutan et al. 2019).
Global climate change has already resulted in large-scale coral bleaching events at increasing frequency causing worldwide reef degradation since 1997. Almost all warm-water coral reefs are projected to suffer significant losses of area and local extinctions, even if global warming is limited to 1.5ºC (IPCC Report, 2019). There are also collections for the aquaria trade where larger individuals (>60 cm TL) are collected for local aquaria and smaller individuals (<60 cm TL) are targeted for export to European aquaria, sometimes up to 60 individuals per shipment.