Otoliths are small, bio-inorganic structures found in the inner ear of fishes. These “earstones” first form in embryo, and then grow incrementally through the daily deposition of alternating proteinaceous and mineral bands. As the chemistry of an individual fish’s ambient environment varies from day-to-day, each increment will then differ, specifically in the amounts of trace-elements incorporated. Ecologists routinely utilise increment trace-element ratios to reconstruct fish environmental histories. Little is known, however, about the structure and composition of the proteinaceous portion of otoliths. Due to this, there is considerable uncertainty as to whether a given trace-element is present through environmental change, or as a necessary component of one of the proteins present. To answer this question, we first sequenced the transcriptome of a southern Australian fish, Acanthopagrus butcheri (Black Bream). This was then matched to proteomic data collected from the separated organic phase of otoliths and endolymph (inner ear fluid) from wild, adult Black Bream. Our work presents the first transcriptome of a sparid fish, as well as identifies novel inner ear proteins present in A. butcheri.