Abstract Particulate organic carbon, nitrogen, and sulfur are produced in surface waters from photosynthesis and regenerated via oxic respiration. When this organic matter reaches anoxic marine environments, regeneration is largely coupled with sulfate reduction. Hydrogen sulfide from microbial sulfate reduction reacts with Fe(II) through various mechanisms to produce several iron sulfides, of which pyrite (FeS 2) is the most stable in marine sediments. As such, sedimentary pyrite may serve as a long term indicator of conditions under which it was formed. In this respect it has been argued that pyrite can be formed in the anoxic water column as well as produced in the underlying sediments, thus affecting any paleoceanographic interpretations using pyrite and other tracers. Despite this important possibility, few direct observations of pyrite formation in the anoxic water column have been reported. Using analytical methods that are capable of detecting nanomolar concentrations of iron sulfides in suspended particles, depth profiles were obtained for iron monosulfide (FeS), greigite (Fe 3S 4), and pyrite in the anoxic water columns of Framvaren Fjord and the Black Sea; profiles of particulate C, N, and S were also acquired. In Framvaren, maximum particulate C and N were found at the oxic/anoxic interface, while the highest concentrations of particulate organic S (POS) were just above this interface. This low C/N organic matter probably lead to the high concentrations of hydrogen sulfide observed in the deeper waters of Framvaren. Pyrite and greigite showed concentration maxima just below the oxic/anoxic interface, while FeS was almost non-detectable. Throughout the anoxic water column, these iron sulfides comprised 73% of the total particulate sulfur, and filtration experiments indicate that much of the iron sulfide particles were <0.4 μm in size. In the Black Sea, particulate C, N, and S profiles were typical of oceanic waters, with maxima in surface waters and decreasing concentrations with depth into the anoxic waters immediately below. Depth coverage for the particulate iron sulfides was limited, but FeS and greigite showed maxima 70 m below the anoxic interface, while the pyrite maximum was near this interface. The sum of these iron sulfides was only 11% of the total particulate sulfur. POS had its highest concentrations in surface waters of both Framvaren and the Black Sea, suggesting production via photosynthesis and relatively rapid regeneration (surface water residence time of 117–356 days). The behavior of FeS and greigite at both sites agreed with thermodynamic predictions, while the abundance of pyrite was controlled by its production rates and mechanisms.