Abstract: Genes and their regulatory networks of the seed plant and fern were compared to elucidate the molecular mechanism of seed development and evolution. A gene regulatory network was built from downloaded seed-specific genes and network data and compared to the genes of Selaginella moellendorffii to find the key net work nodes. One thousand and fifty-three genes were used to build Arabidopsis thaliana seed-specific gene regulatory network, and 969 of them formed a huge and complicated network. There were 39 genes in the dumbbell-shaped core module of the network. An important hub gene, AT1 G54860, was only found in seed plant genomes. Gene AT1-G54860 encoded a GPI membrane anchored protein, which functioneds in the assembly of cell wall, cell signaling,growth and differentiation. This gene was hypothesized to play an important role in seed development and evolution as a“power-switch”.