Ocean currents are an important driver of evolution for sea-dispersed plants, enabling them to maintain reciprocal gene flow via sea-dispersed diaspores and obtain wide distribution ranges. Although geographic barriers are known to be the primary factors shaping present genetic structure of sea-dispersed plants, cryptic barriers which form clear genetic structure within oceanic regions are poorly understood. To test the presence of a cryptic barrier, we conducted a phylogeographic study together with past demographic inference for a widespread sea-dispersed plant, Vigna marina, using 308 individuals collected from the entire Indo-West Pacific (IWP) region. Chloroplast DNA variation showed strong genetic structure that separated populations into three groups: North Pacific (NP), South Pacific (SP) and Indian Ocean (IN) (F’CT among groups = 0.954 – 1.000). According to the Approximate Bayesian computation inference, splitting time between NP and SP was approximately 20,200 years (95%HPD, 4,530 – 95,400) before present. Moreover, a signal of recent population expansion was detected in the NP group. This study clearly showed the presence of a cryptic barrier in the West Pacific region of the distributional range of V. marina. The locations of the cryptic barrier observed in V. marina corresponded to the genetic breaks found in other plants, suggesting the presence of a common cryptic barrier for sea-dispersed plants. Demographic inference suggested that genetic structure related to this cryptic barrier has been present since the last glacial maximum and may reflect patterns of past population expansion from refugia.