Eutrophication is prevalent in shallow water ecosystems worldwide. Ulva is a genus of bloom forming macroalgae that occur in shallow estuaries. Ulva have ecosystem consequences such as Zostera spp. degradation, fish and shellfish declines. The presented study describes a comprehensive survey of Ulva spp. distributed in Jamaica Bay, NY, USA. Using ITS and tufA DNA Barcoding and cytological techniques, we identified the dominant species of Ulva at 8 sites in Jamaica Bay and 1 site in Long Island Sound, CT to match Ulva compressa, U. cf. clathratioides, U. prolifera, U. stipitata, U. laetevirens, and U. lactuca with other sequences world-wide. All samples collected had <1% divergence between species. Ulva stipitata, a compressed tubular species, was found in Jamaica Bay and is the second known occurrence of the species in the Northwest Atlantic. The presented study has management implications because we know the nitrogen storage potential of Ulva spp. from this major bay in metropolitan New York City coastal waters. Modelling the storage of nitrogen in Ulva spp. could be useful for optimal harvesting purposes to manage Ulva blooms.