The level of specialization of endemic island birds to their native habitats could contribute importantly to increase their extinction risk. We used abundance obtained from mist-netting and radio telemetry data from one individual to determine the micro-habitat use pattern of Juan Fernandez Tit-tyrants (Anairetes fernandezianus) within native forest. The tracked male tit-tyrant established its home range exclusively in core native forest areas. Regression models of abundance and Resource Utilization Functions showed strong micro-habitat preferences of tit-tyrants. The abundance and utilization probabilities of tit-tyrants declined with distance to exotic shrub and increased with distance to human created gaps. Natural heterogeneity in micro-habitat conditions also affected the micro-habitat selection pattern, with use probabilities and abundance increasing with proximity to the humid sites dominated by Gunnera peltata. These findings demonstrate that tit-tyrants do not use native forest sites at random. Therefore, the conservation and recovery of the declining tit-tyrant population could be improved by incorporating such micro-habitat preferences in habitat management programs.