With the increasing awareness of environmental protection, it is necessary to develop natural product extracts as antifouling (AF) agents for alternatives to toxic biocides or metal-based AF paints to control biofouling. This paper briefly summarizes the latest developments in the natural product extracts and their derivatives or analogues from marine microorganisms to terrestrial plants as AF agents in the last five years. Moreover, this paper discusses the structures–activity relationship of these AF compounds and expands their AF mechanisms. Inspired by the molecular structure of natural products, some derivatives or analogues of natural product extracts and some novel strategies for improving the AF activity of protective coatings have been proposed as guidance for the development of a new generation of environmentally friendly AF agents.