The divergence of the gnetophytes has been controversial due to the lack of appropriate fossils to calibrate the phylogenetic trees. Here we describe a new macrofossil family, Protognetaceae Y. Yang, L. Xie et D.K. Ferguson, fam. nov., from the Middle Jurassic, consisting of only Protognetum jurassicum Y. Yang, L. Xie et D.K. Ferguson, gen. et sp. nov. This monotypic family displays transitional morphology between Ephedraceae and Gnetaceae. It is similar to the Ephedraceae in the longitudinally striated twigs, the linear parallel-veined leaves decussate at the swollen nodes, and to the Gnetaceae in the lax female spikes and a few sessile female reproductive units (FRUs) verticillately arranged at the nodes. These FRUs are subtended by leaf-like linear bracts, and have an apical short and straight tube. The Protognetaceae provide new evidence to understand the early evolution of the gnetophytes. We reconstructed a phylogeny of gymnosperms based on six DNA markers, and dated the divergence of the gnetophytes with calibration using our new macrofossil. We found that the crown age of the gnetophytes is in the Middle Triassic, the age of modern Ephedra is in the Neogene, and modern Gnetum is dated back to the K/T boundary.