Gene–background interaction is a commonly observed phenomenon in many species, but the molecular mechanisms of such an interaction is less well understood. Here we report the cloning of a maize mutant gene and its modifier. A recessive mutant with a virescent yellow-like (vyl) phenotype was identified in an ethyl methanesulfonate-mutagenized population derived from the maize inbred line B73. Homozygous mutant maize plants exhibited a yellow leaf phenotype after emergence but gradually recovered and became indistinguishable from wild-type plants after approximately 2 weeks. Taking the positional cloning approach, theChr.9_ClpP5gene, one of the proteolytic subunits of the chloroplast Clp protease complex, was identified and validated as the candidate gene forvyl. When introgressed by backcross into the maize inbred line PH09B, the mutant phenotype ofvyllasted much longer in the greenhouse and was lethal in the field, implying the presence of a modifier(s) forvyl. A major modifier locus was identified on chromosome 1, and a paralogousClpP5gene was isolated and confirmed as the candidate for thevyl-modifier. Expression ofChr.1_ClpP5is induced significantly in B73 by thevylmutation, while the expression ofChr.1_ClpP5in PH09B is not responsive to thevylmutation. Moreover, expression and sequence analysis suggests that the PH09BChr.1_ClpP5allele is functionally weaker than the B73 allele. We propose that functional redundancy between duplicated paralogous genes is the molecular mechanism for the interaction betweenvyland its modifier.