Although the use of Bacillus thuringiensis (Bt) as a foliar spray is minimal within New Zealand at present, a considerable effort is being made genetically to incorporate Bt δ‐endotoxin genes into a wide range of important crops, including pasture species, perennial horticultural crops and annual field crops. For several years it has been clear that the major threat to the sustained efficacy of Bt in New Zealand is the evolution of insect resistance. Recognition of this threat has prompted consideration of a range of strategies for preventing and/or managing its possible evolution in pests of specific crops. However, such strategies do not address the critical issue of how we might limit the consequences of Bt resistance if it did evolve, particularly the evolution of resistance in polyphagous pests. Highly mobile polyphagous pests, such as leafroller species, might develop resistance to Bt on one transgenic crop and then disperse, nullifying the effectiveness of a wide range of Bt transgenic crops expressing the same or similar Cry proteins. Pests with resistance to CryIA proteins in transgenic plants might also display significant resistance to Bt biopesticides. To prevent such an eventuality in New Zealand we propose a plan for deploying Bt genes among crops according to an assessment of the risk and consequences of Bt resistance evolving in the insect complexes on these crops. The major elements of this plan are: (i) assess the risk of Bt resistant insects evolving and dispersing out of the crop to infest others; (ii) characterize the diversity of Bt protein binding sites in the guts of key polyphagous pests; (iii) use the above information to deploy Bt genes among different transgenic crops in a pattern that minimizes the chance that any future Bt resistant cosmopolitan pests will be broadly cross‐resistant to other Bt crops and/or Bt biopesticides.