Biomanufacturing of recombinant proteins in the microalgae has become an important field of research owing to sustainability, scalability, safety, and metabolic diversity of the microalgal system. Recovery of the recombinant protein from the host system needs to be devised and established, since the conventional downstream process for recombinant protein extraction is associated with high costs and resources. In a previous study, we have reported two putative signal peptides of C. aponinum using in silico approach. Herein, we evaluated the two secretory signal peptides for heterologous protein secretion in C. aponinum PCC10605. The green fluorescent protein was used as secretory protein and as a reporter. Signal peptides, thermitase and porin, fused with GFP were transformed in to C. aponinum for studying the expression and secretion. Following the antibiotic screening and GFP fluorescence analysis, transformants secreting GFP in the supernatant were validated by using western blotting. The results showed that fluorescence, as measured by FACS analysis and TECAN reader, varied among the two signal peptides and, higher fluorescence was recorded in the 'thermitase SP secreted GFP' supernatant. The thermitase signal peptide may offer as a new gateway for recombinant protein production and secretion in C. aponinum.