DNA was sequenced from sediment traps deployed at three locations in the Pacific Ocean in February 2017. DNA was extracted from bulk sediment trap samples containing RNAlater or an unpreserved brine layer. Individual particles were isolated from polyacrylamide gel layers deployed in sediment traps and DNA was isolated and sequenced from these individual particles. These data were generated to identify genetic remnants of organisms within the sinking particles that transport carbon into the deep ocean.