The composition and concentration of dissolved free amino acid (DFAA) of seawater samples collected in May 2016 from the surface to the hadal zone of the northern region of the Yap Trench were analyzed by pre-column derivatization of o-phthalaldehyde. Results show that the average concentration of DFAA in the study area was 0.47±0.36 µmol/L. In different sampling stations, the concentrations of DFAA with water depth showed complex variation patterns. At the sediment-seawater interface, the concentrations of DFAA in the western side of the trench were obviously higher than that in its eastern side. In the study area, there were no significant correlations between the concentrations of DFAA and the environmental parameters such as concentrations of chlorophyll a (Chl a), dissolved oxygen (DO), pH, and dissolved inorganic nitrogen (DIN), indicating that the concentrations of DFAA in seawater of the trench are affected by many factors, such as photosynthesis, respiration, temperature, pressure, illumination, and circulation. The dominant DFAA are similar in different water layers of sampling stations, including aspartic acid (Asp), glutamic acid (Glu), glycine (Gly), and serine (Ser). The composition of different amino acids, and the relative abundance of acidic, basic, and neutral amino acids might be related to the sources and consumption of various amino acids. Nine pairs of amino acids in the DFAA showed significantly positive relationship by correlation matrix analysis, suggesting that they might share similar biogeochemical processes. The degradation index (DI) of the DFAA in seawater of the Yap Trench could reflect the degradation, source, and freshness of DFAA in the trench to some extents. This is a preliminary study of amino acids from sea surface to hadal zone in the ocean, more works shall be done in different trenches to reveal their biogeochemical characteristics in extreme marine environments.