Phosphine (PH3) resistance in the stored-products insect pests has been reported throughout the world in various insect species, including Rhyzopertha dominica, Tribolium castaneum, and Cryptolestes ferrugineus, leading farmers and fumigators to identify new fumigation tools to control PH3-resistant insect pests in storage facilities. Understanding PH3-resistance mechanisms in insects might contribute to providing clues for the development of new chemicals, including fumigants, to control various PH3-resistant insects. A proteomic study has shown 15 decreased proteins in the PH3-resistant R. dominica (CRD343 strain) in comparison to the PH3-susceptible R. dominica, and among those 15 proteins, dihydrolipoamide dehydrogenase (DLD), a protein involved in the Krebs cycle, was identified (Park et al., 2008). The DLD polymorphisms responsible for genetic resistance have disulfide active sites for PH3 binding and are highly sensitive to arsenic exposure after mutagenesis in insects (R. dominica and T. castaneum) and Caenorhabditis elegans (Schlipalius et al., 2012). Here, two PH3- resistant S. oryzae strains were used to understand the development of PH3 resistance in these insects. Acute toxicity test by PH3 on the two PH3-resistant strains was undertaken followed by ethyl formate inhibition study on cytochrome c oxidase activity. The Lineweaver-Burk plots after inhibition studies showed there were significantly difference in inhibition mode between the resistant strains and the control. The RT-qPCR analysis and the next-generation sequencing of the mitochondrial DNA revealed significant changes in metabolism and energy production. Taken together, the PH3 resistance in S. oryzae was definitely acquired by the overall transformation of biochemical reactions to overcome PH3 toxicity.