Nearly all deep-sea cephalopod life history studies have been completed by examination of specimens collected in the wild. Much of this work is like piecing together a puzzle; knowledge of the life history of many species remains fragmented and hence, taxonomically and phylogenetically confused. Molecular approaches and sequencing technologies are powerful tools for deciphering wild-type cephalopod life history and population dynamics. Use of molecular markers offers additional certainty for identifying specimens damaged during deep-sea collections and can elucidate often cryptic, intra- and interspecific diversity. The research presented in this study assessed broad genetic patterns of biodiversity in deep-sea cephalopods from the Gulf of Mexico and northwestern Atlantic Ocean. This study has two key objectives: [1] to examine intraspecies variation among regionally disjunct subpopulations, comparing collections separated by the Florida Peninsula, and [2] to examine intraspecies variation within deep-sea cephalopods in the Gulf of Mexico. Through Sanger sequencing marker genes COI, 16S rRNA, and 28S rRNA, this study has generated a genetic baseline characterization of deep-sea cephalopods in the Gulf of Mexico, assessed intraspecies genetic variation, and linked morphological identification with DNA barcodes, testing morphological hypotheses of species identification and naming. Results of investigating intraspecies variation within regionally disjunct subpopulations reveal there is no regional distinction between the Gulf of Mexico subpopulations of Vampyroteuthis infernalis, Pyroteuthis margaritifera, and Cranchia scabra, and the Bear Seamount subpopulations in the northwestern Atlantic Ocean. Results of investigating intraspecies variation within the Gulf of Mexico displayed potential for cryptic species, novel sequence records, and large expansions to sequence records for species known to inhabit the Gulf of Mexico. Analysis of intraspecies variation within the Gulf of Mexico facilitated identification of damaged specimens used for this study, but also revealed GenBank database issues of misidentified records, and outdated nomenclature in accession records. Because cephalopods play a central role in most oceanic ecosystems, characteristics like a short average life span and a rapid growth rate mean that cephalopod populations have the potential to serve as an invaluable reflection of ecosystem change.