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Using the phenylpyrazole insecticide, fipronil for selection in the laboratory, a resistant Wenzhou strain of the rice stem borer, Chilo suppressalis (Walker) (Lepidoptera: Crambidae) had an LD50 at least 45.3 times greater than the susceptible Anhui strain. The realized resistant heritability (h2) of 0.213 showed that the tolerant phenotype was moderately heritable and had potential to develop higher tolerance to fipronil. Piperonyl butoxide decreased the effects of fipronil on the mortality of the susceptible larvae with 0.27–0.44 times synergistic rates, but increased the toxicity of fipronil on the resistant larvae with 1.85–2.53 times synergistic rates as compared to that of fipronil alone. The inhibitory effect of piperonyl butoxide on the activity of microsomal O-demethylase was greater in susceptible larvae than in the resistant larvae. The differential synergism of fipronil by piperonyl butoxide in the susceptible and resistant C. suppressalis may be caused by the reduced penetration of fipronil in the lab-selected Wenzhou strain.