The two most fundamental processes generating biodiversity, speciation and immigration, however, counteract each other. Speciation is more likely when immigration is restricted, while speciation cannot be initiated unless immigration occurs to new lands. Therefore, it is important to understand their relative contributions that derived the present biodiversity, yet, there has been no consensus view on it. This is possibly attributed to the fact that geological dynamics, introducing temporal fluctuation on speciation-immigration balance, has not been considered previously. Speciation and immigration could be temporally decoupled by geological dynamics in non-volant (land-dependent) animals (e.g. mammals). Immigration may, on the other hand, overwhelm speciation under geological dynamics in volant animals (e.g. birds). We tested this prediction by reconstructing the histories of 193 Japanese animals (68 mammals and 125 birds). In Japan, land-bridges repeatedly formed and disappeared between the continental mainland, thus, its temporal influence can be easily traced. In mammals, we found temporally clustered divergence events only during frequent land-bridge events, suggesting that immigration and speciation was temporally decoupled. In birds, however, frequent land-bridge events facilitated immigration more than speciation, while speciation was maximized during geologically more stable periods. We concluded that immigration-speciation interaction was greatly impacted by geological dynamics.