We compare the ultrahigh resolution 9.4 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectra of marine dissolved organic matter (DOM) isolated from two sites in the Weddell Sea (Antarctica) obtained by complementary electrospray ionization (ESI) and atmospheric pressure photoionization (APPI). Ions produced by APPI extend to higher carbon unsaturation than those produced by ESI, indicated by higher double-bond equivalents (rings plus double bonds) minus oxygen (DBE-O) values, whereas ESI-generated ions are more oxygenated. Moreover, many sulfur-containing compounds were efficiently ionized by ESI but not detected by APPI. Because the mass spectra obtained by ESI and APPI are significantly different, both are necessary to obtain a more complete description of the molecular composition of marine DOM. © 2010 John Wiley & Sons, Ltd.