C-4 photosynthesis is normally associated with the compartmentation of photosynthesis between mesophyll (M) and bundle sheath (BS) cells. The mechanisms regulating the differential accumulation of photosynthesis proteins in these specialized cells are fundamental to our understanding of how C-4 photosynthesis operates. Cell-specific accumulation of proteins in M or BS can be mediated by posttranscriptional processes and translational efficiency as well as by differences in transcription. Individual genes are likely regulated at multiple levels. Although cis-elements have been associated with cell-specific expression in C-4 leaves, there has been little progress in identifying trans-factors. When C-4 photosynthesis genes from C-4 species are placed in closely related C-3 species, they are often expressed in a manner faithful to the C-4 cycle. Next-generation sequencing and comprehensive analysis of the extent to which genes from C-4 species are expressed in M or BS cells of C-3 plants should provide insight into how the C-4 pathway is regulated and evolved.