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The mysterious deep-sea shrimp Physetocaris microphthalma Chace, 1940 remains a challenge for the understanding of caridean shrimp systematics. Upon first description in 1940, the unique morphology in combination with lack of material made the allocation of P. microphthalma to any family or superfamily difficult, therefore the monotypic superfamily Physetocaridoidea and family Physetocarididae were described. The rarity of the species, only documented a few times in scientific literature, in combination with a circumglobal distribution, makes the advancement of the systematics and biology of this shrimp challenging. Current literature places Physetocaridoidea as a superfamily with a sister relationship to Pandaloidea but this relationship has never been tested using molecular data. Recent expeditions to the northern Gulf of Mexico and north-eastern Pacific Ocean provided fresh material for inclusion in phylogenetic analyses. Here, we used a molecular systematics approach to investigate the phylogenetic placement of this species within the infraorder Caridea and test for cryptic diversity across oceanic basins. We sequenced five genes (12S rRNA, 16S rRNA, H3, NaK and PEPCK) and built phylogenetic trees including specimens across Pandaloidea and other carideans (n = 75) using maximum-likelihood and Bayesian approaches. Our results strongly support the inclusion of P. microphthalma within the family Pandalidae and superfamily Pandaloidea, indicating that the superfamily Physetocaridoidea and family Physetocaridae are not valid. In addition, the inclusion of specimens from the Atlantic and Pacific Oceans does not support evidence of cryptic diversity, suggesting the global distribution of P. microphthalma. This is the first study to provide genetic data for this species, resulting in an updated classification for the infraorder Caridea and highlighting that deep-pelagic species can be rare yet still widely distributed.