We used DNA sequences from 18S rDNA (808 bp) and COI mtDNA (599 bp) to infer evolutionary history of northern groups of the deep-sea mysid genus Pseudomma. The V4–V7 regions of 18S show an average of 1.31% sequence divergence between species. A secondary structure model is constructed and used in phylogenetic analyses to allow for different evolutionary rates in paired and unpaired nucleotide partitions. COI is observed as highly variable with uncorrected p-distance averaging 33%. Phylogenies for these sequences were estimated by maximum-likelihood, Bayesian, and maximum-parsimony analyses. More or less similar tree topologies were obtained for each gene with these methods. Pseudomma longisquamosum was placed in a basal clade, using Parapseudomma and Amblyops as outgroups, but the exact relationship of other basal taxa is less clear when results from the two genes are compared. An ancient presence of Pseudomma in the Tethys Sea is suggested by phylogenetic structure, molecular clock considerations, and present distributions. A well-supported Atlantic clade may have diverged from Indo-Pacific groups in the Miocene because of the closure of the Gibraltar Strait. More recent speciation events are proposed in the Norwegian Sea, and an Arctic intrusion from the North Pacific across the Bering Strait is suggested for the circumpolar species Pseudomma truncatum.