<p>In this study, a two-stage anaerobic ammonium oxidation (anammox) system—including a partial nitritation system with a biological selector (PNBS) and a granular activated carbon-based granule anammox process (GAP) —was used for the treatment of real high-strength rare-earth ammonia wastewater (HRAW). A nitrogen removal rate of 89% on average was achieved at the end of the study with the influent total nitrogen concentration of 2200 mg l<sup>-1</sup>. The nitrogen-loading rate (NLR) of 17 kg N/(m<sup>3</sup>×d) was achieved in the PNBS, and a reduced NLR of 6 kg N/(m<sup>3</sup>×d) was maintained in the GAP. To our knowledge, this is the highest NLR applied to a two-stage anammox system. A genetic analysis of the sludge samples revealed that a <em>Nitrosomonas</em><em> sp.</em> was enriched in the PNBS reactor, while, <em>Kuenenia stuttgartiensis</em><sub>,</sub><em> Uncultured bacterium clone KIST-JJY001</em>, and <em>Uncultured anoxic sludge bacterium KU2</em> were enriched in the GAP reactor.</p>