The annual Zea mays ssp. mexicana L. is a member of the teosinte group and a close wild relative of maize. Thus, Zea mays ssp. mexicana L. can be effectively used in maize breeding. AtCCHA1 is a Mn2+ and/or Ca2+/H+ antiporter localized in chloroplasts in Arabidopsis. In this study, its homolog from Zea mays ssp. mexicana L., ZmmCCHA1, was isolated and characterized. The transcriptional level of ZmmCCHA1 in Zea mays ssp. mexicana L. was repressed in response to excessive Ca2+ or Mn2+. Heterologous functional complementation assays using yeast mutants showed that ZmmCCHA1 mediates Ca2+ and Mn2+ transport. The ZmmCCHA1 protein was localized in the chloroplasts when expressed in tobacco leaves. Furthermore, ectopic overexpression of ZmmCCHA1 in the Arabidopsis ccha1 mutant rescued the mutant defects on growth and the photosynthetic proteins in the thylakoid membranes. Moreover, the photosynthetic phenotypes of Arabidopsis ccha1 mutant at steady-state were greatly but not completely complemented by the overexpression of ZmmCCHA1. In addition, overexpressing the ZmmCCHA1 rescued the sensitives of PSII in the Arabidopsis ccha1 mutant to Mn2+ deficiency or high Ca2+ condition. These results indicate that the isolated ZmmCCHA1 is the homolog of AtCCHA1 and plays a conserved role in maintaining the Mn2+ and/or Ca2+ homeostasis in chloroplasts which is critical for the function of PSII in photosynthesis.