Studies of pollutant impact on the marine environment assume that organic contaminants are anthropogenic in origin. However, many common polychaete worms and sediments contain readily detectable concentrations of brominated natural products that are often analogues of chlorinated anthropogenic contaminants. Both polychaetes and sediments are used extensively in environmental toxicology and monitoring, and the extent to which natural halometabolites may confound these studies is unknown. To characterize further the relationship among infauna, indicator species, and sedimentary halogenated organics, we examined sediments and infauna from a pristine habitat and animals maintained under laboratory culture for haloorganics using gas chromatography/mass spectrometry. Natural haloorganics are a consistent feature of pristine marine soft-bottom habitats, and their spatial and temporal variation correlates with the abundance of infauna that produce these metabolites. Abundant organohalogens are also present in the widespread polychaete indicator species Capitella sp. I and Streblospio benedicti but absent from the marine invertebrate toxicology model Neanthes arenaceodentata. Studies from the individual to the community level within the fields of ecology, toxicology, and environmental chemistry could be readily confounded by failing to consider these novel animal and habitat characteristics.