Glycerol dialkyl glycerol tetraethers (GDGTs) are ubiquitously found in marine sediments. However, their presence, distributions, and sources in the subduction zone are not fully understood. We investigated isoprenoidal GDGTs (isoGDGTs) and branched GDGTs (brGDGTs) in two sediment cores from the southern and northern subduction plates of Mariana Trench, respectively. IsoGDGTs and brGDGTs exhibited covariation in most sediment samples, and total GDGT concentrations reached a maximum at the subsurface sediment depth similar to 10 cm. Concentrations of isoGDGTs and brGDGTs were clearly elevated at depths of similar to 10 and similar to 45 cm. These indicated that microbial activities potentially influenced the production of the specific membrane lipids of archaea and bacteria. We found that the branched and isoprenoid tetraether index and R-b/i values increased with depth profiles of the Mariana subduction zone, suggesting that deeper sediments likely hosted more brGDGT-producing bacteria than crenarchaeol-producing archaea. The extremely high abundance of cyclopentyl rings in brGDGTs was determined in subsurface sediments. We further proposed that most of the brGDGTs in sediments were produced in situ in the Mariana subduction zone. This study highlights that the extremophilic microbial communities of the Mariana subduction zone may represent a significant component of the global carbon cycle.