The community compositions of mangroves in both southeastern coasts of mainland China and west coast of Taiwan share great similarities because of topogeographic reasons and Kandelia obovata, with its higher cold-tolerance,is the dominant mangrove species on either side of the Strait. Therefore, K. obovata populations in Taiwan, China may most possibly derive from that of China southeast coastal areas. However, the colonization route of the northern and southern populations in Taiwan, China and their genetic relationship with that of mainland China have not been reported. In this study simple-sequence-repeat (SSR) markers and approximate-Bayesian-computation (ABC) were applied to trace its origins in the four distribution locations between the Strait. The results showed obvious differentiation among them and the northern part of the mainland southeastern coast illustrated a higher degree than the other three. It was also inferred that the origin of the northern Taiwan, China population could be trance back to circa 29000-48400 years ago, prior to the last glacial period and its genetic structure was the closest to the southern population of China southeast coast, suggesting they may derive from a common ancestor in the south. The northern and southern populations of the Southeast China coast probably coalesced circa 151000-252000 years ago, approximately during the late mid-Pleistocene. The possible implication lies in that the genetic differentiation between the northern and southern populations and their separation may caused by late-Pleistocene climate changes and sea transgression and regression or that they had different origins. Whereas the highest population similarity between the northern and southern Taiwan, China indicates that the southern population was colonized from the north one, and the hypothesis is also supported by the results of approximate Bayesian computation. It can be inferred therefore that the overall colonization route started from southern population of southeast China and migrated with the Kuroshio Branch Current to the north of Taiwan, China before it ultimately colonized in the south. The study is the first one to utilize approximate Bayesian computation to illustrate the origination and colonization route of mangrove populations between Taiwan, China Strait and has provided referential model for mangrove biogeographic research in coastal Southeast China.