The Great Lakes sea lamprey (Petromyzon marinus) control program currently allocates stream treatments to optimize the number of juvenile sea lampreys killed for a given level of control. Although the economic benefits derived from control appear to outweigh the dollars spent on control efforts, optimizing the number of sea lampreys killed will not necessarily optimize the economic benefits provided by the fish communities. These benefits include both non-consumptive and fishery values. We emphasize that the biological damages caused by each juvenile sea lamprey will vary, as will the economic value associated with each host that is killed. We consider issues related to assessing damages due to sea lampreys, taking into account effects on the fish community and fisheries, so as to improve the sea lamprey control program. We recommend a consolidation of information regarding the valuation of benefits, better understanding of variation in host-parasite interactions among the Great Lakes, and integration of the control program with other fisheries management objectives and activities. Adoption of these recommendations should promote lake trout rehabilitation in the Great Lakes, healthy fish communities and prudent use of limited fishery management resources.