Stable natural blue colorants are becoming increasingly popular among consumers. However, natural blue dyes are rare and unstable in foods. C-phycocyanin is a blue-colored protein derived from Spirulina. Unfortunately, its color is not very stable under thermal treatments and low pH conditions. As a result, their use in the food industry is lacking. The goal of this study was to develop a stable C-phycocyanin through genetic engineering. Specifically, the color stability of 48 native (control) and genetically mutated samples of C-phycocyanin produced using E. coli were analyzed. The color stability of the C-phycocyanin samples were monitored using absorbance at 620 nm and fluorescence under various thermal treatments and pH conditions. To measure thermal stability, all samples were heated in a water bath for five minutes at 70 and 90˚C. Color stability against pH changes were measured by dispersing the samples in pH 3 and 5 buffers for up to five days. For all tests, samples were compared to positive and negative controls. Results from this study show that various genetically modified samples of C-phycocyanin have better color stability as compared to the control samples. Stability of all C-phycocyanin samples decreased as the temperature increased from 70 to 90˚C. The samples with a six-histidine tag on the N-terminal of the alpha subunit were most stable under thermal treatment conditions regardless of additional amino acid substitutions. Samples tended to be more stable over time at pH 3 compared to at pH 5. Samples with a six-histidine tag on the N-terminal of the alpha subunit and a six-histidine tag on the C-terminal of the alpha subunit were more stable than other mutations at this pH level. Results from this study show that specific mutations of C-Phycocyanin have better color stability as compared to the positive controls. This indicates that certain modified samples of C-phycocyanin could be of use as a potential natural blue colorant in the food industry.