Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and absorbance spectroscopy were utilized to investigate the molecular composition of marine dissolved organic matter (DOM) from the upper 2000?m water column at the Mariana Trench. Molecular indices, calculated based on the relative abundance of 4699 formulas assigned from FT-ICR MS data, showed depth stratification. The degradation index (IDEG) varied from 0.610 to 0.663 (0.645?±?0.014) in the surface layer to 0.668-0.754 (0.722?±?0.021) in the deep ocean (below 500?m), indicating that the DOM in the deep layer was more refractory than that of the surface layer. This was confirmed by an increase of modified aromaticity index (AImod) from 0.196 to 0.207 (0.200?±?0.003) in the surface layer to 0.213-0.225 (0.220?±?0.003) at depth. Multivariate analysis based on both bulk molecular parameters and relative abundance of individual formulas showed that the molecular composition of DOM was highly stratified and could be well separated into three groups: the upper layer (5-75?m), the middle layer (200?m) and the deep layer (500-2000?m). In addition, surface-enriched and deep-enriched formulas were identified based on Spearman correlation between relative abundance of individual formulas and depth. The surface-enriched formulas were characterized by higher H/C and lower AImod, while deep-enriched formulas showed lower H/C and higher AImod. Variations in AImod and H/C for these formulas indicated that extracellular release (mainly from primary production) and photochemical processes strongly affected the DOM composition in euphotic zone, while microbial processes likely exerted a tremendous influence on the DOM composition at all depths. Moreover, strong correlations between spectroscopic indices (a325, S275-295 and S280-400) and FT- ICR MS derived proxies indicated these two approaches can be integrated to provide valuable information on the molecular characterization of open ocean DOM.