Recent studies have substantially deepened our understanding of the molecular mechanisms underlying symbioses between marine invertebrates and chemosynthetic bacteria. In situ transplant experiments on the vesicomyid clam Archivesica marissinica at the Haima deep-sea seep revealed that the holobiont employs a tiered adaptation strategy in response to sulfide fluctuations: symbionts shift from sulfide oxidation to thiosulfate oxidation to maintain energy supply, the host regulates endosomal–lysosomal pathways to control symbiont abundance, and host hemoglobins possess dual affinity for both oxygen and sulfide, enabling coordinated resource allocation. Multi-omics analyses of Alviniconcha snails from Indian Ocean hydrothermal vents showed that expansion of solute carrier families enhances host–symbiont nutrient transport, myoglobin mediates oxygen storage, and functional zonation of gill filaments finely regulates symbiont digestion and gas exchange. Studies on the family Thyasiridae have filled critical knowledge gaps regarding symbiosis in this taxon. The genome of a deep-sea thyasirid symbiont is highly streamlined (1.53 Mb), retaining complete sulfur oxidation pathways and harboring the capacity for anaerobic respiration. Most notably, the shallow-water thyasirid clam Thyasira tokunagai, inhabiting reducing sediments in the Yellow Sea, also establishes a tightly integrated chemosymbiotic relationship with sulfur-oxidizing Sedimenticola bacteria, fixing inorganic carbon through the Calvin cycle at a measured rate of 29.3 nmol C·clam⁻¹·day⁻¹. These findings compellingly demonstrate that chemosynthetic symbioses are by no means restricted to deep-sea environments—they are also widespread in shallow-water ecosystems, where they play ecologically significant roles.