Introduced algae have become a prominent component of the marine flora in many regions worldwide. In the NE Pacific, the introduced Japanese alga Sargassum muticum (Yendo) Fensholt is common and abundant in shallow, subtidal, rocky habitats, but its effects on subtidal, benthic communities in this region have not previously been studied. I measured the response of native species to experimental manipulation of S. muticum in field experiments in the San Juan Islands of Washington State. Native canopy (brown) and understory (red) algae were more abundant in plots from which S. muticum had been removed, and the native kelp Laminaria bongardiana (the most abundant species of brown alga in the absence of S. muticum) grew more than twice as fast in plots where S. muticum was absent. The negative effects of S. muticum on native algae appear to be a result of shading, rather than changes in water flow, sedimentation, or nutrient availability. S. muticum also had a strongly negative indirect effect on the native sea urchin Stronglyocentrotus droebachiensis by reducing abundances of the native kelp species on which it prefers to feed. My results indicate that S. muticum has a substantial impact on native communities in this region, including effects at multiple trophic levels. Because of their worldwide distribution and capacity to alter native communities, non-indigenous algae are potentially important agents of global ecological change.