<p>The sea urchin <i>Temnopleurus toreumaticus</i> (Leske,&#xa0;1778) is a common species inhabiting the intertidal zones and shallow seas in the China Seas, playing an important role in marine ecosystems. To clarify its population genetic structure and phylogeographic patterns, we collected 163 individuals of <i>T. toreumaticus</i> from seven localities along the Chinese coast, using multiple molecular markers (two mitochondrial genes: COI, 16S rRNA, and one nuclear gene: 18S rRNA) and ten morphological parameters for comprehensive analysis<i>.</i> Phylogenetic reconstructions and haplotype networks based on mitochondrial markers revealed two deeply divergent clades (Clade A and Clade B) within <i>T. toreumaticus</i>. The genetic distances between the two clades were 6.45% for COI and 3.06% for 16S rRNA, exceeding the typical intraspecific distances reported for sea urchins, indicating that <i>T. toreumaticus</i> is a species complex. No significant population genetic structure was detected within either clade, and high dispersal potential likely facilitates gene flow within each clade. The historical isolation of the marginal seas during the glacial period of the Pleistocene might play a crucial role in shaping the cryptic diversity and demographic history of the <i>T. toreumaticus</i> complex. Neutral test and mismatch distribution analysis indicated that Clade A experienced population expansion during the Late Pleistocene period, while the population demography of Clade B was likely more complex. In addition, morphological analysis also revealed consistent differences between the two clades, especially in the size of the apical system, which was highly congruent with molecular delimitation. This study provides comprehensive genetic and morphological evidence for the cryptic divergence within <i>T. toreumaticus</i>, and offers new insights into the population genetics and evolutionary mechanisms of marine echinoderms in the China Seas.</p>