Abstract: Deep-sea cold seeps and hydrothermal vents are two representative chemosynthetic ecosystems that host unique macrofaunal communities, including large invertebrates such as mussels, clams, and tubeworms. These macrofauna commonly form symbiotic associations with internal chemosynthetic bacteria, which oxidize reduced compounds such as methane or hydrogen sulfide to fix carbon and provide primary nutritional source for their hosts. Due to fundamental differences in geological and geochemical settings between cold seeps and hydrothermal vents, biomarkers preserved in macrofaunal tissues exhibit both common and unique characteristics. In this review, we systematically synthesized current knowledge on lipid, amino-acid, and other non-lipid biomarkers in representative symbiotic macrofauna from cold seep and hydrothermal vent environments. Symbiotic macrofauna from the two ecosystems display characteristic chemoautotrophic metabolic signatures; however, significant differences were observed in the composition of lipid and amino-acid biomarkers. These similarities and contrasts directly reflect variations in symbiont type and host adaptive strategy, highlighting distinct metabolic adaptation mechanisms under different chemosynthetic symbioses. By summarizing recent advances in biomarker research from cold seep and hydrothermal vent systems, we elucidated the metabolic adaptations of macrofauna under different symbiotic modes and discussed their broader geological implications. Despite growing research efforts, systematic comparative analyses of biomarker differences between cold seep and hydrothermal vent macrofauna remain limited. Based on available studies, we summarized key biomarker distinctions between the two environments and proposed that future research should expand biomarker frameworks via high-resolution metabolomics, integrated multi-omics analyses, and molecular fossil approaches, thereby to deepen our understanding of chemosynthetic symbioses in deep-sea ecosystems.