This chapter considers threats to the preservation of painted and engraved rock art sites in the Lesser Sunda Islands (LS) (including Timor-Leste) and Maluku Barat Daya (MBD) in eastern Indonesia. These include both natural and human threats. Although these island groups constitute some of the most remote and undeveloped regions in Wallacea, their rock art sites still face a host of anthropogenic and natural threats. These include anthropogenic threats that come with growing island populations and associated development. They also include the potentially damaging effects of a wide variety of natural agents of destruction such as water action, algal, bacterial and mineral growths, and insect and animal activity. Potential mitigating actions and ways of managing these threats are also discussed.