Restoration efforts for lake trout Salvelinus namaycush in Lake Michigan are increasingly being focused on re-establishment of the species in deep water. This focus is based in part on examination of historical records of indigenous lake trout, which suggest that offshore reefs, especially deep reefs, sustained the greatest numbers of lake trout. This focus is also based on the increasing impact of non-indigenous species, such as alewife and round goby, on lake trout survival on shallow reefs. Development of a successful strategy for re-establishing deep-water lake trout in Lake Michigan will require a better understanding of the challenges to a species that evolved in shallow water and whose nearest relatives are shallow-water fishes. The challenges include an annual temperature cycle with fall warming rather than cooling, which may impact reproductive timing and embryo incubation. Deep water presents challenges to fry in that there is no apparent physiological mechanism for producing swim bladder gas and initial filling of the swim bladder at the surface has little impact on buoyancy once a fry returns to depth and the swim bladder is compressed. First feeding is a challenge because there is no local primary production to support a rich prey supply and the phenology of zooplankton prey abundance differs from that in small lakes. We propose that plans for restoration of lake trout into deepwater habitats in Lake Michigan must proceed in concert with research leading to a better understanding of extant deepwater strains in Lake Superior.