Historical fragmentation and a current annual deforestation rate of 1.2% in the Western Ghats biodiversity hotspot have resulted in a human-dominated landscape of plantations, agriculture, and developed areas, with embedded rainforest fragments that form biodiversity refuges and animal corridors. On private lands in the Anamalai hills, India, we established restoration sites within three rainforest fragments (5, 19, and 100 ha) representing varying levels of degradation such as open meadow, highly degraded sites with dense Lantana camara invasion, abandoned exotic tree plantations (Eucalyptus grandis and Maesopsis eminii), and sites with mixed-native and exotic tree canopy. Between 2000 and 2004, we planted annually during the southwest monsoon 7,538 nursery raised seedlings of around 127 species in nine sites (0.15–1.0 ha). Seedlings monitored at 6-monthly intervals showed higher mortality over the dry season than the wet season and survival rates over a 2-year period of between 34.4 and 90.3% under different site conditions. Seedling survival was higher in sites with complete weed removal as against partial removal along planting lines and higher in open meadow and under shade than in sites that earlier had dense weed invasion. Of 44 species examined, survival across sites after 24 months for a majority of species (27 species, 61.4%) was higher than 50%. Retaining regenerating native species during weed clearing operations was crucial for rapid reestablishment of a first layer of canopy to shade out weeds and enhance survival of shade-tolerant rainforest seedlings.