Tropilaelaps mercedesae is an ectoparasite of immature honey bees belonging to the genus Tropilaelaps (Acari: Laelapidae). T. mercedesae has become a major threat to the Western honey bee Apis mellifera in Asia, including Korea, and is expanding its geographical range to northern regions due to global warming. To establish gene resources of T. mercedesae, the whole transcriptome was analyzed by RNA sequencing. An mRNA-focused library was generated from total RNA extracted from the mixed stages using the TruSeq RNA Library Preparation kit and sequenced using the HiSeq 2000 platform. A total of 6.0 Gb reads were obtained with 85% Q30 value. Trimmed sequence data were de novo assembled using the CLC Assembly Cell v 4.2. A total of 64,868 non-duplicate contigs were finally obtained and annotated by the Blast2GO using the NCBI nr database. The most abundant species in the resulting 14,336 Blast hits (22.1%) was Metaseiulus occidentalis, a predatory mite, followed by Ixodes scapularis and Tribolium castaneum, suggesting that the T. mercedesae transcriptome matches well with closely related other arthropod species, including mites and ticks. In order to provide basic information for efficient control and monitoring of potential resistance in T. mercedesae, acaricide target genes were annotated and characterized. One voltage-sensitive sodium channel gene encoding the molecular target of fluvalinate, a pyrethroid acaricide most widely used for the control of T. mercedesae, was identified and its molecular properties were investigated. In addition, other acaricide target genes, including acetylcholinesterase and glutamate (or GABA)-gated chloride channel, were identified and characterized.