The dataset represents the number, the total and the standardized biomass (catch per unit effort) of 94 deep-pelagic fish species collected by pelagic trawling in submarine canyons of the Bay of Biscay slope during the EVHOE scientific cruises on R/V Thalassa in autumn between 2002 and 2019 (https://doi.org/10.18142/8). Fifty-six trawls were conducted at night between 20 m and 2000 m depth. The trawl net was 192 m long with a headline of 76 m and a foot rope of 70 m. The average vertical mean mouth opening was about 24 m and the horizontal opening of about 58 m. The mesh size gradually decreases from very large 8 m meshes at the mouth to 20 mm meshes in the codend. To allow the capture of very small specimens, the trawl is also equipped with a 7.5 m long sock with a 12 mm mesh. The trawl had an average vertical mouth opening of 24 m and a horizontal opening of 58 m. The duration of the haul was 1 hour at 4 kn. The trawl did not have an opening-closing mechanism. Therefore, some individuals might have been caught during the descent and ascent of the gear, however a higher trawl speed on deployment and a low speed on retrieval were implemented to reduce bycatch at shallower depths than the target depth. The biomass per unit effort is standardized by the volume hauled and was calculated by multiplying the vertical and horizontal trawl opening and the distance trawled. Individuals were identified by expert ichthyologists to the species level whenever possible, otherwise they were identified to the genus or family level, especially when individuals were too small or damaged. Species or taxa were counted and most often weighed. When weighing was not possible, an estimate of the average weight of individuals over the whole time series was calculated and the total weight per species was estimated.