The tetrasporophyte of Asparagopsis armata has been previously established as a novel seaweed biofilter for integrated land-based mariculture. The species growth and biofiltration rates were much higher than the values described in the literature for Ulva spp., the most common seaweed biofilter. However, a validation of the advantage of one species over the other requires a study of the performances of these two species in the same system at the same time. In this work, we compared the biofiltration performance and biomass yield of A. armata and Ulva rigida cultivated in the effluents of a fish farm in southern Portugal. Comparisons were performed at different water renewal rates and in two seasons of the year. The maximum total ammonia nitrogen (TAN) removal rates were similar for both species in December (2.7 and 2.8 g TAN m–2 day–1 for U. rigida and A. armata, respectively) and higher for A. armata (6.5 g TAN m–2 day–1 ) than for U. rigida (5.1 g TAN m–2 day–1 ) in May. Higher differences were observed when estimating the nitrogen biofiltration through the organic nitrogen yield (N yield) of the biomass produced, particularly in May. This estimate is directly related with the biomass yield and the N content in the tissue which were always higher for A. armata than for U. rigida. In December, the maximum biomass yields were 71 g dry weight (DW) m–2 day–1 for A. armata and 44 g DW m–2 day–1 for U. rigida, while in May, the yield of A. armata was 125 g DW m–2 day–1 and of U. rigida was 73 g DW m–2 day–1 . This study confirmed that A. armata is indeed a more efficient biofilter than U. rigida. To the best of our knowledge, the production rates reported here are the highest ever reported for macroalgae cultivated in tanks.