Freshwater prawns of the genus Macrobrachium of Taiwan are diverse, rich in amphidromous species, but poor in land-locked and endemic species. The fauna showed higher similarity to those of the Philippine Islands and Ryukyu Islands than that of the China mainland. Based on their geographical distribution patterns in the Indo-Pacific region and their phylogenetic relations reconstructed from the nuclear 28S rDNA sequences, we hypothesize their most likely biogeographical origins and dispersion routes. For the 16 known species of Macrobrachium of Taiwan, 13 species were amphidromous. Their biogeographical origins were: 1) in the eastern region of tropical Southeast Asia islands, dispersing to Taiwan through the Philippines islands for M. australe, M. lar, M. latimanus, M. gracilirostre, M. jaroense, M. esculentum, M. lepidactyloides, and M. placidulum; 2) in the western region of tropical Southeast Asia islands, dispersing to Taiwan through the Philippines and/or mainland China for M. equidens, M. latidactylus, and M. mammillodactylus; 3) in mainland China for M. formosense; and 4) on the island of Taiwan for M. japonicum. For the remaining three species, M. asperulum, a land-locked prawn, and M. nipponense, a non-obligatory amphidromous prawn, originated in mainland China. M. shaoi is the only endemic prawn to Taiwan and its life cycle is still unknown.