Intertidal mites (Oribatida) comprise four families that are distributed worldwide. This study aims to clarify the following three points. (1) The four families of tidal mites each exhibit distinct global distribution patterns: two families span polar to subpolar and temperate zones, while the remaining two families show broad equatorial– warm-temperate ranges. The evolutionary origins and biogeographic roots of these lineages have not been sufficiently elucidated. (2) The Japanese archipelago spans low to high latitudes, extending through subarctic, temperate, and subtropical climate zones. It harbors one family centered in the high-latitude Arctic region and two families concentrated in lower-latitude regions. Although their distributions have often been explained solely by ocean currents, we examine key environmental factors underlying the current distributional boundaries. (3) We provide a comprehensive interpretation of the present-day distributions in light of the geological history of the archipelago and molecular population genetic analyses. Published and unpublished mitochondrial COI sequences and published complete mitochondrial genomes from Japanese oribatid taxa were analyzed, comprising approximately 110 OTUs, for molecular dating and population genetics. Inferred divergence times were compared to major geological events of Japan and the surrounding area’s plate tectonics. (1) Ameronothridae inhabit the subarctic zone of the Northern Hemisphere, Podacaridae the subantarctic zone, and Fortuyniidae and Selenoribatidae the tropical and subtropical regions. Our analyses of complete mitochondrial genomes suggest that the transition from terrestrial to marine habitats occurred independently in three separate regions: the subarctic, the subantarctic, and the tropical–subtropical zones. (2) In Japan, there is a distributional boundary between Ameronothridae, which is centered in high-latitude regions, and the two families concentrated in lower-latitude regions. This boundary corresponds approximately to a mean air temperature of 17°C and a mean sea surface temperature of 19°C. The two low-latitude families in particular are adapted to higher temperatures, with species richness declining progressively toward the north. (3) Molecular population genetic analyses suggest that these distributional boundaries, previously attributed solely to ocean currents, are strongly associated with topography. In particular, subtropical intertidal mites have repeatedly experienced dispersal, fragmentation, local extinction, and recolonization driven by the intense temperature and sea-level fluctuations caused by Pleistocene glacial cycles. These patterns are closely linked to temperature gradients, and the results further suggest that refugial populations persisted in slightly warmer low-latitude areas, serving as source populations for subsequent recolonization.