The Green Lake, Wisconsin, strain of lake trout Salvelinus namaycush was discontinued as a hatchery brood stock in 1976 after Lake Michigan was stocked with the 1975 year‐class. In 1982, a decision was made to restore the Green Lake strain as a production brood stock. Five groups were produced by spawning marked fish that were survivors from the 1976 stocking of southern Lake Michigan. A sixth group was produced from a remnant of the Green Lake brood stock held at the Genoa (Wisconsin) National Fish Hatchery. Hatchery accidents reduced both the number of groups and the effective population number of each group. We studied a procedure for reconstructing a composite Green Lake brood stock from individuals of these six groups. Genetic variability was evaluated by allozyme electrophoresis in five of these groups. Twelve of 18 loci were polymorphic. Allelic frequencies were similar in all five groups; however, significant differences occurred in nine systems. Heterozygosity level (mean ± SE) was lowest in the domestic group (0.119 ± 0.043) and ranged from 0.139 ± 0.043 to 0.166 ± 0.052 in the feral groups. Cluster analysis of genetic distances grouped the four feral groups together, but separate from the domestic group. Progeny from fish captured on Black Can Reef, Lake Michigan, in 1986 and 1988 were the most similar. A modified diallel mating design was developed to produce a composite brood stock from remnant feral and domestic fish. Pooled families from 1991 and 1992 diallel matings will be reared to maturity, then reciprocal crosses of the two year‐classes will be made to form the new composite Green Lake brood stock.