The citrus red mite, Panonychus citri, is known for its ability to rapidly evolve resistance to insecticides/acaricides and to adapt to hosts that produce toxins. To get better insight into the detoxification mechanism of P. citri, two carboxylesterase (CarE) genes, PCE1 and PCE2, were isolated and characterized. PCE1 and PCE2 contained open reading frames of 1,653 and 1,392 nucleotides, encoding proteins of 550 and 463 amino acid residues, respectively. Phylogenetic analyses showed that PCE1 and PCE2 were most closely related to the CarE genes from other phytophagous mites. The transcriptional profiles of two CarE genes among developmental stages (egg, larva, nymph, adult female, and adult male), after exposing to four acaricides (avermectin, azocyclotin, pyridaben, and spirodiclofen) and acid rain were investigated using real-time quantitative PCR (qPCR). The results showed that during development, PCE1 was highly expressed at the egg stage, whereas PCE2 was abundantly expressed at the adult stage of males. The expression levels of PCE1 were highly induced upon exposure to acaricides and acid rain. On the other hand, the expression levels of PCE2 were increased after treatment with avermectin and pyridaben. These results suggest that PCE1 and PCE2 may have distinct roles in different developmental stages and participate in the detoxification of acaricides.