To explore gonad-specific gene transcription in the red abalone Haliotis rufescens, cDNA from mature reproductive tissues was 454-pyrosequenced. A total of 79 877 and 133 850 high-quality reads were generated for females and males, respectively, with an average length of 600 bp. Clustering and assembly of these reads produced a non-redundant set of unique sequences, comprising 2793 and 10 354 contigs, 8581 and 32 175 singletons, respectively, for males and females. In silico gene transcription analysis, comparing the sexes showed that 20% of the differentially expressed transcripts are involved in sex-specific patterns. Gene ontology analysis revealed a higher percentage of metabolic processes associated with females, whereas binding processes and biological regulation were mainly related to male transcriptomes. Single nucleotide polymorphism (SNP) associated with sex-related genes, such as lysin (SNP102), PF (SNP1254) and VTG (SNP876) were discovered and validated through high-resolution melting analysis. This study generated relevant genomic sequence data that might contribute to a better understanding of the various reproductive biological processes occurring in abalone. Once the underlying biological processes are understood, biotechnological methods to control maturation, identify sex and produce monosex lines for abalone aquaculture can be envisioned.