Biozones are routinely used for chronological purposes, but their nature is seldomly questioned. Here, we attempt to find the evolutionary-ecological basis for Iberian rodent biozones for the interval 8.5–2 Ma based on currently available paleontological, stratigraphic and paleoclimatic information. Our comparison of biozone boundary age uncertainty intervals to records of marine SST, δ18O and δ13C, terrestrial hydrological proxies and astronomical parameters suggests an orbitally forced climatic origin for the majority of biozones. Zone boundary ages during the late Miocene are mostly associated with humidity changes during 1.2-Myr obliquity nodes and 405-kyr eccentricity minima. Tectonics and strong regional cooling may additionally explain faunal change during the Messinian (7–5 Ma). A partly reversed pattern characterizes most Pliocene zone boundaries, which are mostly associated with wetter conditions during obliquity nodes and 405-kyr eccentricity maxima. A third configuration culminates in the early Pleistocene and consists of the combination of strong obliquity amplitude maxima and 2.4-Myr eccentricity minima. It is suggested that larger-scale, European Neogene mammal (MN) units have an astronomical basis as well, with an important role of 2.4-Myr eccentricity cycle and the 1.2-Myr obliquity cycle, with the latter becoming especially important after the mid-Miocene cooling (~14 Ma). Whereas rodent events on the Iberian Peninsula during the late Miocene are shaped by replacements within resident communities dominated by dry-adapted clades of true mice (Murinae) and hamsters (Cricetinae), transitions during the cooler Pliocene involve invasions of newly emerging Eurasian clades of ‘microtoid hamsters’ and voles (Arvicolinae) preferring wetter and cooler environments. A new model of stepwise clade displacement is proposed in which the combination of long-period Milankovitch cycles and gradual long-term climatic change allows for the periodic functioning of migration corridors, along which increasingly pervasive dispersal events by members of new clades cause the gradual extinction of old clades.