Since the 1950s, fishery agencies on Lake Michigan have pursued Lake Trout Salvelinus namaycush rehabilitation through Sea Lamprey Petromyzon marinus control, harvest regulations, and by stocking millions of fish annually. Stocking was prioritized at four historically important spawning locations beginning in 1985, and coded wire tags (CWTs) were used to help evaluate performance. We used data from CWT fish captured in fishery-independent surveys from 1998 – 2014 to evaluate relative post-release survival of Lake Trout, estimated by catch-per-unit-effort and corrected for the number of fish stocked (CPUE), across 173 CWT tag lots of the 1994 – 2003 year classes stocked at these four locations. Boosted regression tree (BRT) models were used to assess the relative influence of four variables on Lake Trout CPUE in two age groups (age 4-5 years and 6-10 years) and paired with analyses of variance to test for statistical significance. Genetic strain (29.1%), stocking location (27.8%), mortality at release (23.1%) and predator density (19.9%) had similar influence on the relative survival of younger fish, whereas relative survival of older fish was heavily influenced by stocking location (79.8%). Survival of both age groups was lowest for fish stocked in the Northern Refuge, where the age structure was truncated due to fishery harvest and Sea Lamprey predation. Survival of stocked fish was higher at the Southern Refuge, Clay Banks, and Julian’s Reef, where mortality from sea lamprey and harvest was lower, and where increases in wild Lake Trout have been observed in recent years. Stocked Lake Michigan remnant genetic strains also appeared to survive better than strains from other lakes at these three locations, but strain effects could not be fully disentangled from effects of stocking location, and continued stocking of multiple genetic strains may provide resiliency toward future selection pressures. Continued progress toward rehabilitation will require reducing fishing and lamprey-induced mortality in northern Lake Michigan to build parental stocks of advanced ages as well as balancing efforts among competing management goals.