Technical Abstract: Weed seed persistence in soil can be influenced by many factors, including crop management. This research was conducted to determine whether organic management systems with higher organic amendments and soil microbial biomass could reduce weed seed persistence compared to conventional management systems. Seeds of smooth pigweed and common lambsquarters were buried in mesh bags in organic and conventional systems of two long-term experiments, the Farming Systems Project at Beltsville, Maryland, and the Farming Systems Trial near Kutztown, Pennsylvania. Seed viability was determined after retrieval at half-year intervals for two years. Viable seed half-life of smooth pigweed was lower in the organic than conventional systems in two of four location-experiments, whereas half-life of common lambsquarters was lower in the organic than conventional system in one of four location-experiments, but higher in the organic than conventional system in two of four location-experiments. There were few effects of soil depth on seed persistence, but where they existed, seeds were more persistent at 15 cm than at 5 cm. At the Beltsville location, seed persistence was higher in systems without spring tillage than systems with tillage. Total soil phospholipid fatty acid (PLFA) content was higher in organic systems than conventional systems at both locations, and the organic system at Beltsville was associated with a Gram-negative bacteria dominated community structure. There were few correlations between PLFA biomarkers and seed half-lives in the first experiment, however, there were negative correlations up to -0.64 for common lambsquarters and -0.55 for smooth pigweed at the 5 cm depth at Kutztown in the second experiment. General associations between broad soil microbial metrics and weed seed persistence suggest a potential role of microorganisms in seed mortality in these systems, but more precise research targeted to identifying specific microbial functions causing seed mortality would provide a clearer picture of the role of soil microbes in weed seed persistence.