As a more efficient quantitative method for morphological analysis, geometric morphometrics is applied to the flabellate fossils Flabellophyton including Flabellophyton lantianensis and Flabellophyton strigata from Neoproterozoic Ediacaran Lantian biota, South China. Both traditional morphometric analysis (including diverging angle, length, and width distribution) and geometric morphometric analysis [including superposition of normalized area analysis, non-metric multidimensional scaling (n-MDS), Bray-Curtis similarity cluster analysis (CLUSTER) and analysis of similarities (ANOSIM)] were performed. The results indicate there are great interspecific morphological differences between F. lantianensis and F. strigata, in addition to some intraspecific variations within each species. Here we preliminarily suggest that the previously defined Flabellophyton should be subdivided into 2 genera at least: one marked by the dark transverse striated structure, and the other without. This recharacterization and reclassification work still needs further careful observation and comprehensive analysis with large number of flabellate fossils combining morphology, structure, population, and community-ecology study.