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Resistance management for Bt-transgenic crops relies in part on the production of sufficient numbers of susceptible insects in non-toxic refuges. Simulation models suggested that source-sink dynamics could interact with the structure of refuges to impact the production of insects in these areas. We tested the hypothesis that altering isolation between refuges and transgenic cotton by manipulating the width of refuges embedded within cotton fields would alter the density of Heliothis virescens and Helicoverpa zea eggs oviposited in refuges. Three categories of refuge widths were tested over two years: they included narrow (16–24m wide), medium (32-48m wide) and wide (80–96m wide) refuges. Isolation between the two habitats increased as refuge width increased. In 1996, eggs of H. virescens from H. zea were not distinguished, but a significant increase in the density of eggs and a significant decrease in relative yield (refuge yield compared to the yield from immediately surrounding Bt-cotton) was found as refuge width increased. In 1997, eggs from H. virescens were analyzed separately from H. zea using an ELISA test. The density of H. virescens eggs increased with increasing refuge width, and there was a significant decline in density of H. virescens eggs with increasing distance from the refuge. In contrast, there was no impact of refuge width on the density of H. zea eggs, nor was the slope of a regression of egg density and distance from the refuge significantly different from zero. We suggest that these differences reflect differences in the biology of the two insects.