The Arthrospira maxima, Spirulina major, and Spirulina subsalsa are plenty available in Mexican lakes and ponds. This cyanobacterium is used as an important dietary supplement due to its high protein content and vitamins. However, the most commercial strain in use is A. platensis, and very few reports exist on other Spirulina species from Mexico and their potential phycocyanin production. To use at a commercial scale, it is essential to evaluate native strains in an efficient purification process. In this work, we demonstrated the potential of Spirulina subsalsa for phycocyanin pigment production and purification process, compared with native A. platensis from Mexico. The biomass yield with S. subsalsa was 4.50±0.10 g/Lt, which was higher than A. platensis, which was 1.36 g/lt. The crude phycocyanin pigment from S. subsalsa was 267±0.37 mg/g, whereas 221±0.04mg/g in the case of A. platensis. After partial purification, we found a higher purity grade in S. subsalsa, with a higher yield and a recovery percent of 39.75%. In the case of A. platensis, after partial purification, the recovery percentage was 35.37. After ionic chromatography purification, the purity of phycocyanin was 2.57±0.03 in the case of S. subsalsa, whereas 1.91±0.02 in the case of A. platensis. SDS gel electrophoresis demonstrated two phycocyanin bands showing 17 kDa and 12 kDa in the case of both species. The two-step purification process functions very well for S. subsalsa species, whereas A. platensis demonstrated efficiency with one step. The extracted C-PC from S. Sulsalsa is safe as per the cytotoxicity assay.