A new stygobitic cyclopoid species, Mesocyclops sondoongensis sp. nov. is described from caves in central Vietnam. This is the first cave-dwelling representative of Mesocyclops in SE Asia. Conspicuous features of the new species, such as the narrow lateral arms of the seminal receptacle and the presence of medial spine on leg 1 basipodite, are only shared with the rarus-group in the Paleotropics, but common among the Neotropical representatives. Surface ornamentation of the labrum is similar to that in the Middle American reidae-clade, a basal lineage in Mesocyclops. The basal relationships within Mesocyclops are re-examined herein. Strict consensus tree shows that: i. M. sondoongensis and the rarus-group constitute a clade, which is the sister to all Mesocyclops exclusive of the reidae-group; ii. the Neotropical species and M. edax (North and Middle America) constitute a clade, which is the sister to all Mesocyclops lacking medial spine on leg 1 basipodite and distributed mainly in the Paleotropics. Branching sequence of the trees might be congruent with: i. origin of the genus in Northern Tropical Gondwana, ii. origin of the clade (M. sondoongensis, rarus-group) in India-Madagascar, and dispersal from India to SE Asia in the Eocene when India collided with Asia; iii. New World-Old World vicariance during separation of northern South America from Africa in the Cretaceous.