Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species (C. warmingii and L. guentheri), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii, highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.