In Zea mays (maize), photosynthetic activities are partitioned between two morphologically and biochemically distinct cell types, mesophyll (M) and bundle sheath (BS). These cells are organized as concentric files around the vasculature and functionally cooperate in fixing carbon for photosynthesis. Partitioning of photosynthetic activities between M and BS cells is mediated by cell-specific localization of transcripts and proteins. However, regulation of this process is poorly understood. Here, we utilize two mutants, hcf136 and bsd2, which are selectively disrupted in M or BS cell development, respectively, to dissect the relative importance of sugar, energy metabolites and photosystem II protein complex formation in establishing functional M and BS transcriptional networks. RNA transcript profiling was performed on isolated M and BS cells of WT and mutant siblings, followed by comparative analysis between the two mutants. The results suggest that M and BS transcripts are autonomously regulated by different signals.