This study investigates the endemic centres of Indonesian animals and the biodiversity across geographical gradients. At the same time, it also evaluated different lines suggested for separating the Oriental and Australian faunal region in the Indonesian region. The analyses have mainly used the present-day distribution of terrestrial vertebrates, especially the smallest ranges of species and subspecies. The results show that faunal migration of Oriental and Australian lineages to the Indonesian Archipelago may have been happening since the Palaeocene period and more importantly, island drifts might have facilitated such migration. These events caused major reorganisation of island positions and island forms, which in turn resulted in faunal extinction around the mid-Pliocene. Some islands, especially in the Wallacea region, emerged very late and as a result nowadays they are lacking endemic forms. There are currently at least seven endemic centres, which can be recognised, i.e. Borneo, Java, Sumatra, Sulawesi, North Moluccas, New Guinea and the Lesser Sundas/Banda Arcs. The affinities between these endemic centres revealed that there are two clusters of islands in the Indonesian Archipelago. These different clusters suggest in turn the shifts of biogeographical lines in the Indonesian Archipelago. Furthermore, oscillation in climate, eustatic sea level changes and fluctuations in vegetation in the Quaternary period had much affected the distribution pattern of animals. There was a phase of expansion for montane oak forests, grasslands and woodlands during the period 18,000-14,000 years ago in East Indonesia and 16,500-12,000 years ago in West Indonesia. Such an expansion led to the increased isolation of rainforests and of the faunas adapted to them. These periods are also indicated by the lowering of the tree line which facilitated montane fauna to disperse across lower elevations. At 8,000-9,000 years ago, the climate became warmer and slightly wetter. The mid- to upper montane forests expanded to their full altitudinal range, while montane oak forest, grassland, and woodland areas had contracted. The oscillation in climate, eustatic sea level changes and fluctuations in vegetation in turn determines much the formation of numerous sub endemic centres, which today can be found within the mainland. Recently, there are 14 sub endemic centres on Borneo, 8 on Java, 16 on Sumatra, 14 on Sulawesi and 14 on New Guinea. From the conservation management point of view, the identification of such sub endemic centres would generate valuable information for the protection effort.