Abstract
Island biogeography provides a crucial framework for interpreting global biodiversity patterns; however, the distinctive dynamics of continental islands remain underexplored relative to those of volcanic oceanic islands. This knowledge gap obscures our understanding of species dispersal and evolution, particularly on small continental islands whose connectivity has been modulated by Quaternary sea‐level oscillations. Here, we integrate double‐digest restriction‐site‐associated DNA (ddRAD) sequencing with mitochondrial COI and 16S rRNA data to investigate the phylogeography, population structure, demographic history and ecological niche of the narrowly distributed freshwater crab Nanhaipotamon nanriense inhabiting mainland and nearby islands in southeastern China. Our analyses revealed strong genetic differentiation, highlighting a deeply divergent island lineage isolated by a narrow marine channel and an inland lineage isolated by the Minjiang River. Demographic reconstructions indicated significant population expansions during lower sea level in the Pleistocene, followed by population contractions correlated strongly with post‐glacial sea level rise in the Holocene. By synthesising genomic, demographic and ecological evidence, our study demonstrates how marine inundation, riverine barriers and glacio‐eustatic cycles jointly shape the genetic and distributional patterns of continental island freshwater species and also provide critical insights for conservation strategies.