Only few studies exist that investigate the dynamics of deep-sea dissolved organic matter (DOM) derived from hydrothermal vents. In this study, we provide first insight into the molecular composition of DOM associated with Indian Ocean hydrothermal systems covering the full range from hot focussed endmember fluids over diffuse fluids to open ocean hydrothermal plumes and deep seawater. We combined geochemical analyses with molecular characterization of DOM using ultra-high resolution mass spectrometry (FT-ICR-MS). We studied two vent systems with fluids venting >330 °C and up to 97% of hydrothermal endmember: the Kairei vents (Central Indian Ridge) with brine phase separation, and the newly discovered Pelagia vents (South-East Indian Ridge). The hot fluids in both systems were highly enriched in dissolved Fe, Si, K, Li, Mn and Zn compared to seawater. The molecular composition of DOM from hot fluids differed substantially from that of diffuse fluids and plumes, in which the composition was highly dominated by the seawater DOM signature. Low O/C ratio average in hot fluids (<0.38) indicated potential input of more reduced (O-poor) DOM compounds from the vents into the surrounding seawater, independently of the vent location and of whether the fluid has undergone phase separation. To test the importance of pure thermal degradation, we compared our samples to fluids subjected to abiotic thermal degradation under laboratory conditions and we observed that our natural samples largely differed (>94% Bray Curtis dissimilarity) from the experimental ones, suggesting additional degradation processes of organic compounds at the Indian Ocean hydrothermal systems.