Laodelphax striatellus is an important pest of rice due to not only sucking rice seedlings, but also transmitting serious plant viruses. Among various kinds of insecticide groups (carbamates, organophosphorus, neonicotinoids, etc.), carbofuran, a systemic carbamate insecticide, has been most extensively used to control rice pests including L. striatellus, resulting in widespread carbamate resistance in Korea and other Northeast Asia countries. To identify the genes associated with carbofuran resistance, we obtained a 14-fold higher resistant strain (SEL9) from the mixed-field population (SEL0) by consecutive selection. A transcriptome-based analysis was conducted and differentially expressed genes (DEG) were compared between the SEL9 and SEL0 strains. A total of 96,185,150 reads were analyzed, of which 62,860,430 reads were mapped. From these reads, 15,356 transcripts were annotated. A total of 327 up-regulated and 275 down-regulated genes were identified in the resistant SEL9 strain compared to SEL0 strain by DEG analysis. Gene ontology (GO) analysis was performed using DEGs showing statistical significance (P < 0.05). The GO analysis identified 1,320 genes in biological process group, 1,100 genes in cellular component group and 428 genes in molecular_function group.