The objective of the study was to assess the distribution of native and invasive tunicates in the fouling community of shellfish aquaculture gear along the U.S. east coast of the Atlantic. Since the 1980s, several species of invasive tunicates have spread throughout the coastal waters of the North American east coast and have become dominant fouling organisms on docks, boat hulls, mooring lines, and in shellfish aquaculture. Invasive and native tunicates negatively impact shellfish aquaculture through increased maintenance costs and reduced shellfish growth. While the presence of alien tunicates has been well documented at piers, harbors, and marinas, there are few published reports of invasive tunicate impacts to aquaculture. We surveyed shellfish aquaculture operations at Martha’s Vineyard, Massachusetts and shellfish aquaculturists in other areas along the North American east coast and report high levels of fouling caused by seven invasive, three native, and two cryptogenic species of tunicates. All study sites were fouled by one or more tunicate species. Biofouling control treatments varied among aquaculture sites and were effective in removing tunicates. Invasive and native tunicates should be considered when assessing the economic impacts of fouling organisms to the aquaculture industry.