The Anammox process was used to treat the effluent generated in an anaerobic digester which treated the wastewater from a fish cannery once previously processed in a Sharon reactor. The effluents generated from the anaerobic digestion are characterised by their high ammonium content (700–1,000 g NH+4-N m−3), organic carbon content (1,000–1,300 g TOC m−3) and salinity up to 8,000–10,000 g NaCl m−3. In the Sharon reactor, approximately 50% of the NH+4-N was oxidised to NO−2-N via partial nitrification. The effluent of the Sharon step was fed to the Anammox reactor which treated an averaged nitrogen loading rate of 500 g N m−3· d−1. The system reached an averaged nitrogen removal efficiency of 68%, mainly limited due to the nonstoichiometric relation, for the Anammox process, between the ammonium and nitrite added in the feeding. The Anammox reactor bacterial population distribution, followed by FISH analysis and batch activity assays, did not change significantly despite the continuous entrance to the system of aerobic ammonium oxidisers coming from the Sharon reactor. Most of the bacteria corresponded to the Anammox population and the rest with slight variable shares to the ammonia oxidisers. The Anammox reactor showed an unexpected robustness despite the continuous variations in the influent composition regarding ammonium and nitrite concentrations. Only in the period when NO−2-N concentration was higher than the NH+4-N concentration did the process destabilise and it took 14 days until the nitrogen removal percentage decreased to 34% with concentrations in the effluent of 340 g NH+4-N m−3 and 440 g NO−2-N m−3, respectively. Based on these results, it seems that the Sharon–Anammox system can be applied for the treatment of industrial wastewaters with high nitrogen load and salt concentration with an appropriate control of the NO−2-N/NH+4-N ratio.