Abstract: We have profiled the diversity of functional genes encoding diagnostic enzymes of aerobic ammonia and methane oxidation in the Nankai Trough sediments. Bulk DNAs were extracted from 79 deep-sea sediment core samples, off-central Japan. Total 429 clones of the genes encoding ammonia monooxygenase, amoA(β) and particulate methane monooxygenase, pmoA, yielded ten and two operational units, respectively. Patchy distributions of the clones were uncorrelated to known geological and geochemical features of the sediments.