Hypnea musciformis that are harvested from natural beds and introduced Kappaphycus alvarezii are the two main sources of raw material for the production of carrageenan in Brazil. The daily growth rate (DGR) and carrageenan yield (CY) of both species were evaluated in vitro and in the sea to assess the feasibility of cultivating H. musciformis as a complement or as an alternative to the production of K. alvarezii. The DGR of H. musciformis (10.8 ± 0.6% day−1) was higher than the DGR of K. alvarezii (5.6 ± 0.3% day−1) in vitro, and the CY extracted using NaOH (62.3 ± 0.15%) was better than using KOH (32.0 ± 0.3%). In eutrophic medium, the DGR of H. musciformis (9.4 ± 2.1% day−1) was higher than that of K. alvarezii (5.0 ± 1.2% day−1). However, in this condition, the CY was similar for both species (50.2 ± 3.5%), and both species were effective in removing nutrients (30% NH4+, 18% NO2− and 2.4% PO43−). H. musciformis did not survive when cultivated in the sea, neither in monospecific nor in multispecific cultivation. Moreover, K. alvarezii grew better in monospecific cultivation throughout the year (from 1.73 to 5.15% day−1) except during the wet period and the CY was high in both cultivation types (33.7–50.8%). We conclude that the cultivation of H. musciformis is not an alternative to K. alvarezii on the Brazilian southeastern coast. However, the results in vitro suggested its use as a complementary source of carrageenan or as a biological filter.