The sunken carcasses of great whales (i.e., whale falls) provide an important deep-sea habitat for more than 100 species that may be considered whale-fall specialists. Commercial whaling has reduced the abundance and size of whales, and thus whale-fall habitats, as great whales were hunted and removed from the oceans, often to near extinction. In this article, we use a metapopulation modeling approach to explore the consequences of whaling to the abundance and persistence of whale-fall habitats in the deep sea and to the potential for extinction of whale-fall specialists. Our modeling indicates that the persistence of metapopulations of whale-fall specialists is linearly related to the abundance of whales, and extremely sensitive (to the fourth power) to the mean size of whales. Thus, whaling-induced declines in the mean size of whales are likely to have been as important as declines in whale abundance to extinction pressure on whale-fall specialists. Our modeling also indicates that commercial whaling, even under proposed sustainable yield scenarios, has the potential to yield substantial extinction of whale-fall specialists. The loss of whale-fall habitat is likely to have had the greatest impact on the diversity of whale-fall specialists in areas where whales have been hunted for centuries, allowing extinctions to proceed to completion. The North Atlantic experienced dramatic declines, and even extirpation, of many whale species before the 20th century; thus, extinctions of whale-fall specialists are likely to have already occurred in this region. Whale depletions have occurred more recently in the Southern Hemisphere and across most of the North Pacific; thus, these regions may still have substantial "extinction debts," and many extant whale-fall specialists may be destined for extinction if whale populations do not recover in abundance and mean size over the next few decades. Prior to the resumption of commercial whaling, or the loosening of protections to reduce incidental take, the impacts of hunting on deep-sea whale-fall ecosystems, as well as differential protection of the largest whales within and across species, should be carefully considered.