Sex is increasingly seen as a continuous, rather than a dichotomous trait. Sex is phenotypically plastic in many marine fishes and results from environmentally-sensitive differential gene regulation. Bluehead wrasse (Thalassoma bifasciatum) are highly-social reef fish and well-studied models of sexual plasticity. These diandric, protogynous (female-first) hermaphrodites have three sexual morphs as adults whose development is plastic and socially cued. Bluehead wrasse mature as male (primary males) or female, but each have the capacity to become dominant (secondary) males later in life. Large, brightly coloured secondary males actively defend and court a harem of females, whereas primary males are female-mimics that employ a ‘sneaker’ mating strategy. Using whole-transcriptome RNA-sequencing (RNA-seq) we have explored the molecular basis of plastic sexual phenotypes in bluehead wrasse brain and gonad. Differential expression analysis identified thousands of genes important in the maintenance of the primary male, secondary male, and female phenotypes. Brain expression profiles of primary males reflect their female-like behaviour, not their male sex. Secondary male brains were most different. We find that isotocin (homologue of mammalian oxytocin) is overexpressed in secondary males, supporting recent evidence for a regulatory role in teleost social interactions, especially those related to dominance and rank. Gonadal expression profiles were strongly sex-biased, although secondary males upregulated genes involved in androgenesis and in the maintenance of secondary sexual characteristics (i.e., colouration and territoriality). Further investigations into the molecular basis of sexual plasticity are now underway, including transitions between alternative phenotypes and comparisons of gene expression patterns in evolutionarily divergent systems.