Simulation were conducted to guide development of resistance management strategies aimed at prolonging the usable life of B. thuringiensis (Bt) endotoxins in multiple cropping situations, where different crops expressing Bt endotoxins are host plants for a common pest. We used the New Zealand apple and clover model ecosystem to explore the relative impact on the rate of resistance development of varying levels of cross-resistance between different toxins expressed in these 2 potentially Bt-transformed crops. These 2 crops are hosts for a complex of leaf-rollers in New Zealand, including the light-brown apple moth, used here as the model pest. Cross-resistance was varied between 0.0 and 0.5 (zero to partial cross-resistance) to allow for the case in which selection by one plant has a potential effect on resistance to the toxin in another plant. The largest factor affecting the evolution of resistance was the total habitat area occupied by transgenic orchards. The proportion of the clover habitat that was transformed was also an important factor, even in the absence of cross-resistance. The effect of increasing the proportion of the second transformed crop (clover) acted on resistance evolution mainly by reducing the external refuge of susceptibility for the transgenic orchards. Hence, the ecological implications of reducing the available source of susceptible insects from clover, which can help to slow resistance development in the orchard ecosystem, had a more significant impact than the presence of cross-resistance. Partial cross-resistance between different toxins in the separate crops was overall of relatively minor importance. These simulations have implications for deployment decisions for individual transformed crops in multiple cropping systems, where there is the potential for the crops to serve as refugees for each other. These decisions may need to focus less on cross-resistance between toxins, than on economic trade-offs between the relative roles of individual crops as refugia maintaining susceptibility in the system as a whole.