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[Display omitted] • The origin of this largest water strider reached the divergence time of the genus within Gerridae. • The "Hainan Island shifting" is first supported by the phylogeography aquatic insect evidence. • ASRR fault triggered the "North-South component" genetic pattern in G. gigas. Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the "north–south component" genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting. [ABSTRACT FROM AUTHOR]