Naled-intoxicated methyl eugenol (ME) is commonly used to control oriental fruit flies, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), in Taiwan. However, non-responsiveness to ME and pesticide resistance in oriental fruit flies may reduce control efficacy. In this study, mark-recapture experiments were used to analyze the effects of naled-intoxicated ME on field and naled-resistant fly strains. ME non-responsiveness was tested in field, naled-resistant, and susceptible strains and pyrosequencing techniques were used to detect frequencies of point mutations on organophosphate resistant alleles in field strains. Finally, the effects of fipronil-intoxicated ME were analyzed to determine whether control efficiency could be enhanced through the use of alternate pesticides. Control efficiency of naled-intoxicated ME was found to be significantly lower in the field and resistant strains compared to the susceptible strain. ME non-responsiveness was found to be 1.7–1.9% in our lab-reared strains (both naled-resistant and susceptible) and 3.4–4.3% in field strains. Results of our pyrosequencing study found frequency of resistant alleles in captured male field flies to be significantly lower than that of the original population, indicating that it is highly probable that resistant flies may escape from traps. Finally, capture rates of naled-resistant flies increased when naled was replaced with fipronil in attractants, showing that use of pesticides with different modes of action could possibly increase control efficiency of intoxicated ME attractants.