The limited information available on pre-oil spill deep-sea biodiversity has been a severe impediment to properly assessing impacts of the DWH event on the meso- and bathypelagic ecosystems of the Gulf of Mexico. Furthermore, available pre-spill information is based mainly on static “snap-shots” surveys of this still incompletely documented biodiversity. It is now becoming apparent that the deep pelagial contains an immensely diverse, dynamic and potentially functionally novel ichthyofaunal community uniquely adapted to this ecosystem. A key component of the DEEPEND Consortium project is to 1) expand knowledge of the diversity of this ichthyofaunal community, 2) resolve the substantial uncertainties in taxonomic affinities and descriptions of taxa inventoried before the spill, and 3) provide DNA barcodes to assist biodiversity surveys related to general ecosystem function and potential, future oil-spill impacts. We report here on our assessment of the deep ichthyofaunal diversity based on COI DNA barcoding of samples collected during DEEPEND cruises in 2015 and 2016. Of the 1,136 fish samples barcoded to date, nearly 60% demonstrated a concordance between assigned morphotaxonomy and DNA barcodes available in the Barcode of Life Database (BOLD), providing confidence in their morphospecies descriptions and assignment. Five percent of samples, comprising fish early life stages (ELF), were able to be assigned to species level based on barcode matches with adult stages, thus providing an opportunity to develop morphological taxonomic keys for these ELFs. Nearly 21% of the samples, however, provided DNA barcodes that either did not match any species, matched more than one species, or demonstrated lack of concordance between morphospecies identified by DEEPEND taxonomy experts and morphospecies in the BOLD. These uncertainties highlight the incomplete nature of deep-sea fish taxonomy in the Gulf of Mexico, including the presence of cryptic species.