A locally isolated co-culture of two photosynthetic species [Chlorella vulgaris (Chlorophyta) and Leptolyngbya sp. (Cyanobacteria)] displayed enhanced growth when compared to a Chlorella monoculture; however, the biological mechanisms driving such improvement are currently not well understood. To investigate these mechanisms, this study examined the differential gene expression in the Chlorella between the co-culture and the monoculture. Suppression subtractive hybridization was performed between mRNA from Chlorella in the co-culture and in a monoculture, and 105 genes were identified as being putatively differentially expressed. Nine of these genes, corresponding to the key functional categories of energy, metabolism, and protein synthesis, were further examined using quantitative real-time PCR and showed differential regulation of photosystem I and photosystem II and upregulation of stress-response genes and a gene encoding an oil-globule-associated gene in the co-culture Chlorella. This differential gene expression study of a Chlorella/cyanobacteria co-culture will aid in the development of culture strategies capable of taking advantage of these differences for the production of biomass and bioproducts of interest. Knowledge of the underlying genetic causes of the changes in growth and productivity of the species in co-culture provides insights on possible target genes for optimization of the culture.