Molecular clock and megafossil bearing reproductive features indicate remarkable discrepancy on minimum age of Ephedra L. Three different explanations at least are present on the conflicts: Paleogene bottleneck, extinction of ancient lineages, and frequent gene exchanges in the genus. This study indicates that extinction of ancient lineages together with frequent gene exchanges may account for the conflict between molecular and megafossil assessments. Modern species alone are inadequate to phylogenetic reconstruction of the genus.