The species boundary may be ambiguous for the genetic admixture and similar morphology in incipient species. The features are resulted from recent gene flow and large amounts of ancestral polymorphisms and may further challenge the taxonomy. Cycas sect. Asiorientales, composed of Cycas taitungensis and C. revoluta, mainly distributed in Taiwan and the Ryukyu Archipelagos, have recently diverged with reciprocal paraphyletic relationships. Previous evolutionary inferences were based on few genetic markers and incomprehensive population samplings, and the morphological comparisons were incomplete due to long-term taxonomy misunderstanding of C. taitungensis. This calls into question the taxonomy and population genetics between these two species. Here, we used genome-wide SNPs with comprehensive population samplings to infer the geographic mode of speciation by approximate Bayesian computation (ABC) in two species. The individual tree was reconstructed for species delimitation and gene flow inferences. The morphometrics of diagnostic traits was incorporated for taxonomy reappraisal. Overlapped morphological variations and undistinguished genetic clusters by continuous gene flow rejected the allopatric speciation. The individual tree further implied asymmetric gene flow from Taiwan to northern Ryukyu islands, possibly due to the transoceanic vegetative dispersal by the northward Kuroshio Current and long-distance pollen flow. The above evidence suggests that neither C. taitungensis nor C. revoluta is an independent, monophyletic lineage. According to the principle of priority in nomenclature, C. taitungensis should be treated as a synonym of C. revoluta.