Abstract: The psaA gene is a fundamental protein-coding gene of photosystem Ⅰ. Using the relaxed molecular clock model, positive selection model, and co-evolutionary analysis, we attempted to unravel its evolutionary pattern. Results indicated that the full-length coding sequences of psaA from fern species could be novel sites for the reconstruction of phylogenetic trees, and could exhibit high posterior probability when combined with the full-length coding sequences of rbcL. The current research also illustrated that the PSAA protein had 29 positively selected amino-acid sites aggregated into 16 co-evolution groups, indicating that ferns had internally modified their photosystem Ⅰ to enhance their ability to adapt to the photosynthetic environment after the rise of angiosperms.