Pyridaben is a mitochondrial electron transport complex I inhibitor. The H110R mutation in the PSST subunit has been reported as a major factor in pyridaben resistance in the two-spotted spider mite, Tetranychus urticae. However, backcross experiments revealed that the mutant PSST alone conferred only moderate resistance. In contrast, inhibition of cytochrome P450 (CYP) markedly reduces resistance levels in a number of highly resistant strains. It was reported previously that maternal factors contributed to the inheritance of pyridaben resistance in the egg stage, but the underlying mechanisms have yet to be elucidated. Here, we studied the combined effects of the PSST H110R mutation and candidate CYPs, as metabolic resistance factors, on pyridaben resistance in T. urticae. We found that the maternal effects of inheritance of resistance in the egg stage were associated with CYP activity. Analysis of differential gene expression by RNA-seq identified CYP392A3 as a candidate causal factor for the high resistance level. Congenic strains, where the alleles of both PSST and CYP392A3 were derived from a resistant strain (RR_i; i = 1 or 2) and a susceptible strain (SS_i) in a common susceptible genetic background, were constructed by marker-assisted backcrossing. RR_i showed upregulation of CYP392A3 and high resistance levels (LC50 > 10,000 mg L-1), while SS_i had LC50 < 10 mg L-1. To disentangle the individual effects of PSST and CYP392A3 alleles, we also attempted to uncouple these genes in RR_i. We conclude that given the variation in LC50 values and expression levels of CYP392A3 in the congenic and uncoupled strains, it is likely that the high pyridaben resistance levels are due to a synergistic or cumulative effect of the combination of mutant PSST and associated CYPs, including CYP392A3, but other yet to be discovered factors cannot be excluded.