Branched glycerol dialkyl glycerol tetraethers (brGDGTs), originally linked to terrestrial bacteria for paleoenvironmental reconstructions, are now also known to be produced by marine bacteria. However, the distribution patterns and environmental controls of marine-sourced brGDGTs remain poorly understood, limiting their applicability in marine settings. Here, we analyzed sediments from the South China Sea (n = 45, 3-4574 m depth) and compiled a marine dataset (n = 1274, 0-10,840 m depth) to investigate brGDGT distributions in the global ocean. We find that brGDGT cyclization increases with depth <200 m but decreases markedly at greater depths. After excluding terrestrially influenced samples, marine-sourced brGDGTs exhibit a strong, consistent negative correlation between cyclization and water depth-both regionally and globally. In contrast, isomerization and, to a lesser extent, methylation increase with depth. Marine brGDGTs differ fundamentally from their terrestrial counterparts in composition, index relationships, and environmental controls, reflecting distinct bacterial assemblages and/or adaptation strategies shaped by the contrasting ecosystems. Therefore, conceptual frameworks developed for soil brGDGTs cannot be directly applied to marine realms. However, the observed structural shifts-declining cyclization and increasing isomerization and methylation-correlate with water depth, bottom-water temperature, and surface productivity, and likely reflect microbial responses to the cold, high-pressure, and nutrition-limited conditions of the deep ocean.