Angiosperm genes sharing a conserved phosphatidylethanolamine-binding (PEPB) domain have been shown to be involved in the control of shoot meristem identity and flowering time. The family is divided into three subfamilies, FT-like, TFL1-like and MFT-like. This study is focused on the evolution of the MFT-like clade, suggested to be ancestral to the two other clades. We report that the bryophyte Physcomitrella patens and the lycopod Selaginella moellendorfii contain four and two MFT-like genes respectively. Neither species have any FT or TFL1-like genes. Furthermore, we have identified a new subclade of MFT-like genes in Angiosperms. Quantitative expression analysis of MFT-like genes in Physcomitrella patens reveals that the expression patterns are circadian and reaches maximum in gametangia and sporophytes. Our data suggest that the occurrence FT and TFL1-like genes, is associated with the evolution of seed plants. Expression data for Physcomitrella MFT-like genes implicates an involvement in the development of reproductive tissues in the moss.