Abstract The deep-sea hydrothermal vent is one of typical extreme environments on Earth that assembles with the early life circumstance. The alvinocarid shrimps comprise the predominant faunal biomass of various hydrothermal ecosystems, representing the key elements of hydrothermal communities of vent fields. Few molecular studies have examined the phylogenetic position, origin and evolutionary history of alvinocarid shrimps because of the limited availability of this taxon for genetic analyses. On the basis of three mitochondrial genes, three nuclear genes, and 12 selected alvinocarid species, our study is the first to secure the placement of alvinocarids within the infraorder Caridea. The results revealed that alvinocarid shrimps may have the closest deep-sea relatives, which originated earlier from shallow water. This result is consistent with the extinction/repopulation hypothesis. The divergence time estimates indicate that hydrothermal vent alvinocarid shrimps colonized the vent ecosystems in Early Oligocene (34.60 Mya). The widespread extinctions of deep-sea faunas during the Late Cretaceous/Early Tertiary created opportunities for invasion of these habitats by the modern taxa. Our analyses suggest that the Western Pacific Ocean with complex back-arc basins was more likely to serve as a pivotal role as a centre of dispersal for the alvinocarid shrimps. Then they invaded into the Atlantic by circumglobal colonization westwards through the Indian Ocean, and invaded into the East-Pacific Ridge, respectively. Our conclusion suggest that the geological processes and dispersal mechanisms discussed here will play an important role revealing the origin and the evolution of the chemosynthetic-fauna in deep-sea hydrothermal vents.