A clear insight into large-scale community structure of planktonic copepods is critical to understanding mechanisms controlling diversity and biogeography of marine taxa, owing to their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed with results from previous morphology-based studies. However, large-scale metabarcoding approach could detected community changes even under stable environmental conditions, including changes in the north/south subtropical gyres and east/west areas within each subtropical gyre. There were strong effects of epipelagic environment on mesopelagic communities, and community subdivisions were observed in the environmentally-stable mesopelagic layer. In each sampling station, higher operational taxonomic unit (OTU) numbers and lower phylogenetic diversity were observed in the mesopelagic layer than in the epipelagic layer, indicating a recent rapid increase of species numbers in the mesopelagic layer. The phylogenetic analysis utilizing representative sequences of OTUs revealed trends of recent emergence of cold-water OTUs mainly distributed at high latitudes with low water temperatures. Conversely, high diversity of copepods at low latitudes was suggested to have been formed through long evolutionary history under high water temperature. The metabarcoding results suggest that evolutionary processes have strong impacts on current patterns of copepod diversity, and support the “out of the tropics” theory explaining latitudinal diversity gradients of copepods. Both diversity patterns in epipelagic and mesopelagic showed high correlations to sea surface temperature; thus, predicted global warming may have a significant impact on copepod diversity in both layers.