BACKGROUNDLaboratory‐selected resistant strains of Euschistus heros to thiamethoxam (NEO) and lambda‐cyhalothrin (PYR) were recently reported in Brazil. However, the mechanisms conferring resistance to these insecticides in E. heros remain unresolved. We utilized comparative transcriptome profiling and SNP calling of susceptible and resistant strains of E. heros to investigate the molecular mechanism(s) underlying resistance.RESULTSThe E. heros transcriptome was assembled, generating 91,673 transcripts with a mean length of 720 bp and N50 of 1795 bp. Comparative gene expression analysis between the susceptible (SUS) and NEO strains identified 215 significantly differentially expressed (DE) transcripts. DE transcripts associated with the xenobiotic metabolism were all up‐regulated in the NEO strain. The comparative analysis of the SUS and PYR strains identified 204 DE transcripts, including an esterase (esterase FE4), a glutathione‐S‐transferase, an ABC transporter (ABCC1), and aquaporins that were up‐regulated in the PYR strain. We identified 9,588 and 15,043 non‐synonymous SNPs in the PYR and NEO strains. One of the SNPs (D70N) detected in the NEO strain occurs in a subunit (α5) of the nAChRs, the target‐site of neonicotinoid insecticides. Nevertheless, this residue position in α5 is not conserved among insects.CONCLUSIONSNeonicotinoid and pyrethroid resistance in laboratory‐selected E. heros is associated with a potential metabolic resistance mechanism by the overexpression of proteins commonly involved in the three phases of xenobiotic metabolism. Together these findings provide insight into the potential basis of resistance in E. heros and will inform the development and implementation of resistance management strategies against this important pest.This article is protected by copyright. All rights reserved.