The overexploitation of the world's biomes for natural products calls for the prioritization of biologically important ecosystems for conservation. Here we show that limestone karsts are “arks” of biodiversity and often contain high levels of endemism. Humans have exploited karsts for a variety of products and services, but unsustainable practices have caused population declines and extinctions among site-endemic taxa. Limestone quarrying is the primary threat to karst biodiversity in Southeast Asia, where quarrying rates exceed those in other tropical regions. Several socioeconomic, political, and scientific issues undermine the stewardship of these karsts. Mitigation of these problems will involve (a) better land-use planning to prevent karst resources from being exhausted in developing regions, (b) comprehensive assessments of a karst's economic and biological value before development, (c) improved legislation and enforcement to protect karst biodiversity, and (d) increased research and activities to promote public awareness of the importance of karsts and the threats facing them.