Squamous cell esophageal cancer presents a significant health burden in many developing countries around the world. In South Africa, this disease is one of the most common causes of cancer-related deaths in black males. Because this cancer is only modestly responsive to available chemotherapeutic agents, there is a need to develop more effective therapeutic agents for this cancer. Marine organisms are currently regarded as a promising source of unique bioactive molecules because they display a rich diversity of secondary metabolites. Some of these compounds have significant anticancer activity, with a few of these currently in phase I and II clinical trials. We report here an ongoing program to screen marine organisms collected from subtidal benthic communities off the coast of southern Africa for activity against cultured esophageal cancer cells. Of the 137 extracts tested, 2.2% displayed high activity (score = 3) and 11.7% displayed moderate activity (score = 2) against cultured esophageal cancer cells. Our results suggest that sponges had a higher hit rate (21.9%) than ascidians (7.1%). Using activity-directed purification, seven previously described compounds and four novel compounds, with varying activity against esophageal cancer cell lines, were isolated from the sponges Axinella weltneri, Aplysilla sulphurea, and Strongylodesma aliwaliensis. The results of this study suggest that subtidal benthic marine organisms collected off the coast of southern Africa hold potential for identifying possible drug leads for the development of agents with activity against esophageal cancer.