Abstract:To understand the molecular mechanisms of ecological responding to terrestrial habitat in gymnosperm species, 53 representative species, belonging to four subclasses of gymnosperms, were selected to molecular evolutionary analysis based on psbA gene coding sequences. Firstly, the phylogenetic tree under geological timescale was established based on relaxed molecular clock model. Secondly, the positive selection signal among PSBA were detected by the estimated ω values by using six models, including MEC/JTT, MEC/cpREV, M5, M7, M8 and M8a. Then, the co-evolutionary network of amino acid sites within the PSBA was investigated by Bootstrap method. The results indicated that the species differentiation process from phylogenetic tree of gymnosperms along the timescale supported to previous studies. The three amino acid sites (13, 19, 243) in PSBA protein endured positive selection during the evolutionary history of gymnosperm species. Certain pairs of site within PSBA protein evolved into a co-evolutionary network. Therefore, the psbA sequences have the potential to be DNA marker during the establishment of the phylogenetic relationship of gymnosperms. The modification of PSBA protein by the site adaptation and protein intra network might be an important factor benefits the adaptive evolution of gymnosperm species against the terrestrial habitat.