‘Wreckfish’ a collective of species belonging to the family Polyprionidae, are an important commercial fishery and have significant aquaculture potential. Until now, genomic or transcriptomic information for any species within the genus Polyprion has either remained unpublished or is non-existent. Using Illumina HiSeq, we compared the transcriptomes of hāpuku (Polyprion oxygeneios) ovaries to explore developmental stage-specific variations underlying their reproductive physiology. We sought to identify differentially expressed genes and the associated shifts in biological pathways between previtellogenic and early vitellogenic ovaries. Ovarian tissue was repeatedly biopsied by gonopore cannulation from the same females (n = 3) throughout oogenesis. Reproductive status of initial biopsies was confirmed as being previtellogenic and that in biopsies collected eight weeks later as early vitellogenic. A de novo hāpuku transcriptome was assembled (146,189 transcripts) from RNA-Seq data without a reference genome. On average, each tissue sample contained 17.5 million trimmed reads. Gene annotation was 80% when using BLASTX against Genbank Non Redundant database. Fifty-three transcripts were differentially expressed within the FDR of 0.05 when previtellogenic and early vitellogenic ovaries were compared; this reduced to 35 differentially expressed genes when transcript duplications were pooled. Among these were genes tentatively associated with the electron transport chain, lipid metabolism, steroidogenesis and mineral/solute transportation. These data provide a snap-shot into stage-specific physiological events during oogenesis in the ovary of a teleost and an extensive molecular resource for research on species in the Genus Polyprion.