The green anole (Anolis carolinensis) has been introduced to the Ogasawara Islands, Japan, and has adversely affected native fauna through predation and competition. To eradicate green anoles, adhesive traps for capture and Teflon™-sheet fencing to restrict movement have been used, however, their efficiency needs to be improved. Using behavioral experiments, we evaluated colors that would attract green anoles to traps and repel them from fences. We also conducted similar experiments on the native snake-eyed skink (Cryptoblepharus nigropunctatus) to establish color preferences in an effort to reduce bycatch. We presented choices of 2 out of 6 colored papers (blue, brown, green, purple, red, yellow) to green anoles and 3 colored papers (blue, brown, red) to snake-eyed skinks to observe which color of paper the animals walked on first. Both species chose blue significantly less often than the other colors (blue was chosen only in 29% of runs). Green anoles demonstrated a preference for brown, whereas snake-eyed skinks favored red. Our results suggested that using blue Teflon™-sheet fence might reduce the transborder crossing rate of green anoles. Furthermore, bycatch of native snakeeyed skinks may be reduced by changing the adhesive trap color to brown, from the currently used red.