Restoration by natural successional processes after removal of perturbations may not be feasible for many degraded ecosystems. Controlling major ecological threats such as non-native ungulates is often a critical first step toward restoring native communities but past degradation, interactions with alien species and abiotic features may create conditions requiring additional intervention to ensure effective conservation. We monitored a series of fenced plots within diverse mesic forest on western Kauai in the Hawaiian Islands from 1998 to 2005 to determine the effects of ungulate removal on native and alien plant species. Relative to unfenced control plots, germination of seedlings and frequency of understory species of both native and alien species increased in the fenced plots. Density of both native and alien canopy and understory species declined more in unfenced than fenced plots, but density of native species declined more than alien species density in both fenced and unfenced plots. In fenced plots, the frequency of larger alien woody species and cover of an alien, mat-forming fern species increased over time, indicating that fencing may encourage alien species that could interfere with regeneration of native species. Our study suggests that effective conservation of this and other remnant native Hawaiian forests will require both ungulate exclusion, removal of alien plant species with especially detrimental effects on native species, and proactive restoration programs for native species without natural sources of propagules. As the effects of invasive species continue to escalate, continental ecosystems lacking high endemism may also require similar interventions to preserve their biodiversity.