The Eastern Redfish (Centroberyx affinis) is not recovering from recent fishing pressure, whereas the Bight Redfish (Centroberyx gerrardi) has fully recovered. Numerous hypotheses, including degree of fishing pressure, climate related stressors, or some combination of the two, have been suggested to explain the difference between the two species. We conducted a series of genomic investigations to determine whether we could find evidence to support either hypothesis. We compared the genome contents of the two fishes and other related taxa, and found no evidence to suggest any difference in susceptibility to climate related pressures. We also used genome resequencing of 61 Eastern Redfish collected from a recent oceanographic voyage, and 10 samples from the Australian National Fish Collection, to examine potential fishing pressure. Analysis of SNP’s indicate a single, well-mixed population across the survey area with minimal population structure. The demographic history was reconstructed with SMC++ and GONE. These indicate a recent population bottleneck, coinciding with a historic change in fishing gear. The runs of homology also indicate increased inbreeding in recent samples, with a greater proportion of 1-5 Mb homologous sections in recent samples compared to historic ones. Taken together, the studies lend support to the idea that prolonged and ongoing fishing pressure, perhaps in combination with other stressors, is hampering the recovery of this species.