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Analysis of the palynofacies and miospore thermal alteration indices (TAI) of sediments from ODP Site 808 in the Nankai Trough was undertaken to determine (1) the source, depositional environment, and diagenesis of organic matter in the accreted sediments, and (2) the thermal structure and history of the prism and its relationship to fluid flow. Using the Hartax classification system, two palynofacies were recognized in the sedimentary sequence. Facies 1 occurs within the upper 600 m of trench-wedge turbidites (sedimentation rate > 1 km/m.y.) and contains >50% inertite particles. The rest of the assemblage is dominated by well-preserved phytoclasts and contains small amounts of poorly preserved phytoclasts and well-preserved scleratoclasts. Facies 2 occurs within the Shikoku Basin hemipelagites (600-1300 m below seafloor; sedimentation rate <150 m/m.y.) and contains over two-thirds inertite particles. The rest of the assemblage is dominated by poorly preserved phytoclasts. Miospores and marine phytoplankton compose only a small percentage of both palynofacies. Degraded organic matter is most noticeable in Facies 2, whereas its presence in Facies 1 is overshadowed by the high influx of well-preserved primary organic matter. Most of the degraded organic matter and inertite is interpreted to be reworked. Some of the degraded organic matter may be primary, and may have experienced more biodegradation and thermal alteration in Facies 2 than in Facies 1. TAI values indicate an immature stage of organic maturation (< 2) down to about 900 mbsf. Below this, samples show an increase with depth to a mature stage, reaching peak levels of about 3 just above basement. Samples from within the thrust fault and decollement zones do not show levels of maturity significantly greater than those of surrounding samples, leaving uncertain whether hot fluids have migrated along these fault boundaries in the past.