C4 photosynthesis is a carbon concentration mechanism that has evolved multiple times across plants as an adaptation to low atmospheric CO2 and hot and dry environments. The molecular mechanisms underlying C4 photosynthesis are complex and involve the coordinated expression of many genes. Here, we investigated the co-expression patterns of genes involved in C4 photosynthesis in the C3 species Arabidopsis thaliana and Taranaya hassleriana and the C4 species Gynandropsis gynandra. Using publicly available transcriptomic data, we constructed gene co-expression networks for C3 and C4 species. We found that the co-expression networks of the C3 species were more similar than that of the C4 species, suggesting that this method can be utilized in a phylogenetic framework. In addition, we identified several interesting patterns of co-expression within and across the networks. For example, leaf-based phosphoenolpyruvate carboxylase (PEPC), a key enzyme in the C4 pathway, appeared loosely correlated with the Calvin Cycle in Arabidopsis and increasingly in Tarenaya. This copy of PEPC is a part of the syntenic locus from which C4-acting PEPC in Gynandropsis is recruited. Additionally, we observed that ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RBCS) copies were not co-expressed within Gynandropsis as they were in the C3 networks. This could indicate a different regulatory mechanism for RBCS in C4 species. Finally, we found that the mean co-expression was lower in C4 species compared to C3. This may reflect the more specialized nature of the C4 pathway and the cell-specific regulation required for its function. In conclusion, our study provides insights into the gene co-expression networks underlying C4 photosynthesis. These findings have important implications for understanding the evolution and regulation of this key process in plants.