Squat lobsters (Galatheoidea and Chirostyloidea), a diverse group of decapod crustaceans, are ubiquitous members of the deep-sea fauna. Within Galatheoidea, the genera Munida and Munidopsis are the most diverse, but accurate estimates of biodiversity are difficult due to morphological complexity and cryptic diversity. Four species of Munida and nine species of Munidopsis from cold-water coral (CWC) and cold seep communities in the northwestern Atlantic Ocean (NWA) and the Gulf of Mexico (GOM) were collected over eleven years and fifteen research cruises in order to assess faunal associations and estimate squat lobster biodiversity. Identification of the majority of specimens was determined morphologically. Mitochondrial COI sequence data, obtained from material collected during these research cruises, was supplemented with published sequences of congeners from other regions. The phylogenetic analysis of Munida supports three of the four NWA and GOM species (M. microphthalma, M. sanctipauli, and M. valida) as closely related taxa. The fourth species, Munida iris, is basal to most other species of Munida, and is closely related to M. rutllanti, a species found in the northeastern Atlantic Ocean (NEA). The majority of the nine species of Munidopsis included in our analyses were collected from chemosynthetic cold seep sites from the GOM. While seep taxa were scattered throughout the phylogenetic tree, four of these species (Munidopsis livida, M. similis, M. bermudezi, and M. species A) from the NWA and the GOM were part of a large eighteen-species clade that included species collected from Pacific Ocean chemosynthetic habitats, such as hydrothermal vents and whale falls. Shinkaia crosnieri was the sister taxon to the chemosynthetic clade, and M. livida was the most basal member of this clade. Munidopsis sp. B, an undescribed species with representative individuals collected from two GOM chemosynthetic sites, exhibited the largest genetic distance from other northern Atlantic species. Generally, intraspecific diversity was lower and patterns of haplotype diversity more simple in species of Munidopsis relative to Munida. This study puts two genera of NWA and GOM squat lobsters into a population genetic and phylogenetic context with regard to biogeography and habitat to enhance understanding of the history and evolutionary trajectories of these morphologically and ecologically diverse groups.