The two-spotted spider (Tetranychus urticae) is one of the most serious pests worldwide and has developed resistance to almost all types of acaricides. Various mutations on acaricide target and detoxification genes and their duplication (including overexpression) have been identified since the completion of T. urticae genome analysis. The mutations are mainly observed in functionally important domains (i.e. transmembrane, cellular loops and catalytic triad, etc.), which likely confer acaricide resistance directly or indirectly. Gene duplication was found on major detoxification and insecticide target enzymes, such as cytochrome P450, glutathione S-transferase, ABC-transporter, UDP-glycosyltranferase and acetylcholinesterase (AChE). Interestingly, co-occurrence of both mutation and gene duplication (especially, single gene amplification) was found in AChE, which possibly explains the compensatory role of gene duplication to minimize the fitness cost mediated by point mutations. Such mutation and duplication traits associated with resistance can be utilized as molecular markers for the determination of resistance levels based on the quantitative sequencing and real-time PCR.