Gaseous sulfide intrusion into seagrasses growing in sulfidic sediments causes little or no harm to the plant, indicating the presence of an unknown sulfide tolerance or detoxification mechanism. We assessed such mechanism in the seagrass Zostera marina in the laboratory and in the field with scanning electron microscopy coupled to energy dispersive X-ray spectroscopy, chromatographic and spectrophotometric methods, and stable isotope tracing coupled with a mass balance of sulfur compounds. We found that Z. marina detoxified gaseous sediment-derived sulfide through incorporation and that most of the detoxification occurred in underground tissues, where sulfide intrusion was greatest. Elemental sulfur was a major detoxification compound, precipitating on the inner wall of the aerenchyma of underground tissues. Sulfide was metabolized into thiols and entered the plant sulfur metabolism as well as being stored as sulfate throughout the plant. We conclude that avoidance of sulfide exposure by reoxidation of sulfide in the rhizosphere or aerenchyma and tolerance of sulfide intrusion by incorporation of sulfur in the plant are likely major survival strategies of seagrasses in sulfidic sediments.