Rats (Rattus rattus, Rattus norvegicus, Rattus exulans) are important invaders on islands. They alter vegetation indirectly by preying on burrowing seabirds. These seabirds affect vegetation through nutrient inputs from sea to land and physical disturbance through trampling and burrowing. Rats also directly affect vegetation though consumption of seeds and seedlings. Seedling communities on northern New Zealand islands differ in composition and densities among islands which have never been invaded by rats, are currently invaded by rats, or from which rats have been eradicated. We conducted experimental investigations to determine the mechanisms driving these patterns. When the physical disturbance of seabirds was removed, in soils collected from islands and inside exclosures, seedling densities increased with seabird burrow density. For example, seedling densities inside exclosures were 10 times greater than those outside. Thus the negative effects of seabirds on seedlings, by trampling and uprooting, overwhelm the potentially beneficial effects of high levels of seed germination, seedling emergence, and possibly seed production, which result from seed burial and nutrient additions. Potential seedling density was reduced on an island where rats were present, germination of seeds from soils of this island was approximately half that found on other islands, but on this island seedling density inside exclosures was 7 times the density outside. Although the total negative effects of seabirds and rats on seedling densities are similar (reduced seedling density), the differences in mechanisms and life stages affected result in very different filters on the plant community.