The dataset contains polychaete abundance data belonging to the family Polynoidae sampled using epibenthic sledge, ROV and box corer (BC; 0.25 m2) within the eastern Clarion Clipperton fracture Zone (northeast Pacific), an area currently being explored for polymetallic nodules. Macrobenthic samples were collected onboard RV Sonne during expedition SO239 in 2015. Four exploration contract areas (BGR, IOM, GSR and Ifremer) and one "Area of Particular Environmental Interest" (APEI#3) were sampled. Eight out of twelve epibenthic sledges samples were fully processed. All polynoids heads have been counted, sequenced and identified. Identifications were realized using morphology and DNA (COI, 16S and 18S genes) leading to morphospecies in most cases (species-level). DNA sequences are available in GenBank or BOLD databases with their respective codes in this dataset.