Background The freshwater species in Taiwan Island have been documented originated from mainland China and Japan Islands multiple times and by multiple colonization routes. Moreover, the sequences from mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used as DNA barcoding to identity species. This study used the COI sequences to identify Neocaridina species in Taiwan and examine their geographical and temporal origins. Results In total, 479 specimens were collected form 35 localities, which almost covers all rivers in Taiwan. The ML tree displayed that all sequences were assorted into 13 taxa (clades), and all sequences in Taiwan were assorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species in Taiwan declined recently. Conclusions All results support that (1) there are four Neocaridina species in Taiwan and they correspond to N. davidi , N. saccam , N. ketagalan and an undescribed Neocaridina species ( N. sp .); (2) these four species colonized Taiwan Island by four colonization events; (3) N. sp . colonized Taiwan before the Taiwan Island developed its shape and then restricted in East Taiwan; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from Japan Islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan lastly; and (6) the cyclic glacial and landform changes shaped the colonization events and population structures of Neocaridina species.