**ABSTRACT:** Rachycentron canadum, popularly known as cobia, is a marine teleost species with great productive potential worldwide, especially in Brazil. Nevertheless, there is a shortcoming regarding gene sequence information for this species in public databases, which hinder the development of more comprehensive investigations, employing molecular biology techniques and gene expression profiling for biomarker identification. In this study, we report the first de novo transcriptome assembly of cobia liver, in an attempt to improve the availability of genes sequences for this important commercial species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101.789 unigenes and 163.096 isoforms, with an average length of 950.61 and 1617.34 nt, respectively. Comparisons against six different databases resulted in functional annotation for 125,993 of these elements (77.3%), providing relevant information regarding the genomic content of R. canadum, which shall assist in future nutrigenomics and other applied studies in the production of this important commercial fish species.
