Summary Threespine stickleback (Gasterosteus aculeatus) and ninespine stickleback (Pungitius pungitius) are both species complexes with many unique and reproductively isolated biological species throughout their range. Both complexes exhibit phenomenal morphological and ecological diversity, including rare phenotypes, in the Cook Inlet Basin in Southcentral Alaska. The Cook Inlet threespine stickleback radiation has been used intensively since the early 1990s to study the genetic and behavioural mechanisms of rapid evolution and speciation, loss of skeletal elements and armor structures, body shape evolution, evolution of development and developmental abnormalities, behavioural evolution, life history evolution, trophic ecology, parasitism, genetic structure and function, and effects of environmental contaminants. Unique populations from both species complexes should be conserved to protect the scientific investment in these radiations and their future utility for research. Many of these populations are now threatened by invasive northern pike (Esox lucius). Northern pike have already caused the local extinction of a rare, weakly-armored threespine stickleback in Prator Lake, and pike are a potential future threat to threespine stickleback in nearby Bear Paw Lake, the source population for the stickleback genome project. Other threats in the Cook Inlet Basin include salmonid stocking in isolated lakes, human impacts on water quality, water withdrawals for human use, and climate change. These threats should be addressed through targeted pike eradication and educational programs on introduced species, a new lake stocking policy that incorporates stickleback conservation, discontinuation of ichthyocide use, research to improve water quality, restrictions on water withdrawals, and a comprehensive stickleback monitoring program. The goals of these actions should be to secure the future viability of special research populations, as well as the maintenance of phenotypic diversity within both stickleback radiations.