Chlorophyll (Chl) content, especially Chl b content, and stomatal conductance (Gs) are key factors that greatly affect net photosynthetic rate (Pn). Setaria italica, a diploid C4 panicoid species with a simple genome and high transformation efficiency, has been widely accepted as a model in photosynthesis and drought-tolerance research. In the current study, Chl content, Gs, and Pn of 48 Setaria mutants induced by ethyl methanesulfonate were characterized. A total of 24, 34 and 35 mutants had significant variations in Chl content, Gs, and Pn, respectively. Correlation analysis showed that positive correlation exists between increased Gs and increased Pn, and a weak correlation between decreased Chl b content and decreased Pn was also found. Remarkably, two mutants behaved significantly decreased Chl b content but increased Pn when compared that of Yugu 1. Seven mutants behaved significantly decreased Gs but non-decreasing Pn when compared that of Yugu 1. The current study thus identified various genetic lines, further exploration of which would be beneficial to elucidate the relationship between Chl content, Gs and Pn and the mechanism underlying why C4 species are efficient at photosynthesis and water saving.