Porphyridium spp. is a debated family that produces phycoerythrin (PE) for use in multiple industrial applications. We compared the differences in the biochemical composition and phycoerythrin yield of P. cruentum and P. purpureum by conventional and green extraction technologies. The protein content in P. cruentum was 42.90 ±1.84% w/w. The omega-3 fatty acid (FA) was highlighted by eicosapentaenoic acid (EPA, C20:5, ω-3, ~9.74 ± 0.27% FA) and arachidonic acid (ARA, C20:4, ω-6, ~18.02 ± 0.81% FA) represented the major omega-6 fatty acid. Conversely, P. purpureum demonstrated a higher lipid content (17.34 ± 1.35% w/w) and an FA profile more saturated in palmitic (C16:0, 29.01 ± 0.94% FA) and stearic acids (C18:0, 50.02 ± 1.72% FA). Maceration and freeze/thaw were the conventional methods, whereas microwave (MW) and ultrasound (US) served as green procedures for PE extraction under the factorial-design methodology. Aqueous solvents, extraction-time and power were the main factors in the statistical extraction designs based on Response-Surface Methodology (RSM). Overall, the PE extraction yield was higher (2-to 6-fold) in P. cruentum than in P. purpureum. Moreover, green technologies (US > MW) improved the PE recovery in comparison with the conventional methods for both of the microalgae. The maximum PE yield (33.85 mg/g) was obtained under optimal US conditions (15 min and buffer solvent (PBS)) for P. cruentum. Finally, we proved the biochemical differences between the red microalgae and ratified the advantages of using green extraction for PE because it reduced the processing times and costs and increased the economic and functional-applications of bioactive compounds in the industry.