The Amami Islands in southern Japan host many endemic species. The small Indian mongoose H. auropunctatus (MG) invasion since 1979, caused populations decline of Amami Rabbit P. furnessi, Amami Woodcock S. mira, Amami Ishikawa’s frog O. splendida and other endemics in the 1990’s, while the MG expanded its population. A MG control project since 2000 successfully has excluded the MG to a very low density by 2014. This suppression has resulted in the initial recovery of severely affected animal populations. However the population and range of endemic species is still small, and other invasive species, such as cats F. catus and black rats R. ratus, continue to damage the native ecosystem. Additionally there is a constant threat of new invasions to the Amami Islands. Our research shows that the top predator Amami Jay G. lidthi breeding success depends on the dominant oak C. sieboldii acorn production as much as predation. Therefore conservation plans should consider both short and long-term effects and potential interaction by both invasive species and other natural factors. Mountain road, which has isolated and dried up natural forest stands, and maybe also the intrusion of many invasive alien species including humane being into the forest, should be reformed to fit nature conservation.