Despite the long history of drug discovery from natural sources, the marine environment, which covers 70% of the Earths surface, is still relatively unexplored. Intense competition for limited resources drives the evolution of specific and potent chemical defenses distinct from their terrestrial counterparts. Based on this rationale, we recently began screening extracts derived from marine invertebrate and cyanobacterial samples for BACE-1 inhibitors in a chemiluminescent enzyme-fragment complementation (EFC) assay. The results of this broad screening are presented here, along with our progress towards the development of a secondary LC-MS homogeneous affinity assay. Incubation of the extracts active in the EFC assay with BACE1, subsequent isolation of the enzyme-inhibitor complex and then analysis of the small molecule inhibitor by LC-MS rapidly links a chemical structure to biological activity. This approach enables the rapid targetorientated discovery of BACE-1 inhibitors from marine sources.