Dissolved organic matter (DOM) in petroleum refinery wastewater is an extremely complex mixture. A better understanding of chemical compositions of DOM at the molecular level is necessary for the design and optimization of wastewater treatment processes. In this study, two largely different DOM samples, one from a petroleum refinery wastewater and the other from the Suwannee river water, were characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled with positive-/negative-ion electrospray ionization (ESI), and positive-ion atmospheric pressure photoionization (APPI). For wastewater DOM, a total of 6226 molecular formulae were assigned in the three ionization modes. However, only 1182 molecular formulae were common in all three mass spectra, indicating that the techniques were highly complementary in the types of molecules they ionize. Acid O_x (x = 1–9) and basic N₁O_x (x = 0–2) classes were dominant in the wastewater DOM detected in negative-ion and positive-ion ESI mode, respectively. And the wastewater DOM contains considerable amounts of polycyclic aromatic hydrocarbons that did not respond to ESI but can be ionized selectively by APPI. Compared with riverine DOM, the refinery wastewater DOM has a higher molecular complexity and is more enriched in hydrocarbon, and nitrogen- and sulfur-containing compounds. The results show that the major components of refinery wastewater DOM were distinctive from those of the natural organic matter. Though not quantitative, the results obtained by various ionization techniques were found to be complementary, and are helpful to our understanding of the selectivity of different ionization techniques as well as the molecular compositions of DOM.