The contemporary distribution and population genetic structure of species are affected by past geological and climatic events, as well as evolutionary history and ecological traits of the species. We investigated the population genetic structure at spatio-temporal scale and demographic history of three cicada species (tribe Cicadini), Yezoterpnosia nigricosta, Tanna japonensis and Euterpnosia chibensis, inhabiting different habitats. Adult samples of Y. nigricosta were collected from 8 locations and evaluated temporal genetic structure in each location over 6 years at longest. Moreover, we collected 677, 426, 131 individuals for Y. nigricosta, T. japonensis and E. chibensis, respectively, and examined the wide scale genetic structure in Japan. We employed maternally-inherited mitochondrial (mt) DNA and biparentally-inherited nuclear DNA variations (microsatellites and single nucleotide polymorphisms). We also explored morphological variations using a deep learning approach. The temporal genetic structure was detected in mtDNA or nuclear DNA variations, depending on the locations. In the wide scale analyses for Y. nigricosta, we detected 154 mtDNA haplotypes, revealing 11 regional groups with a major genetic gap around Kinki region. The mtDNA haplotypes distribution in western Japan showed complex phylogenetic relationships. For example, the individuals in Mt. Gozaisho (Mie Pref.) population were genetically closer to the samples in the Hokkaido and Tohoku region than the western Japan populations and the haplotypes detected in Mt. Odaigahara (Kii Peninsula) were genetically closer to Kyushu populations than Shikoku populations. On the other hand, the genetic structure based on nuclear DNA comprised 5 clusters and the largest genetic differentiation was found between northern and southern Tohoku region and the effective population size of the northern group was smaller than the southern group. Since their habitats, cool temperate forests, are continuously distributed in eastern Japan, but isolated in western Japan, past population expansion and shrinkage episodes related to past climatic oscillations could shape the complex genetic structure. Moreover, the deep learning based morphological analysis revealed an ability to identify the sex and some genetic groups. T. japonensis showed no clear genetic structure except one local haplotype specific to the Sea of Japan side of the Tohoku region. One major haplotype dominated most of the species’ distributional range in E. chibensis and the haplotypes detected in the islands south of Yakushima Island were genetically differentiated by islands. We will discuss the relationship of the past expansion history between these cicada species and their major host forest ecosystems.