| Summary: | Phycoerythrin, a special photosynthetic pigment, is widely used as fluorescent dye and has lots of underlying beneficial effects on health. A marine red microalga <i>Porphyridium</i> is considered as the potential feedstock for phycoerythrin production. However, the phycoerythrin-related properties of <i>Porphyridium</i> have not been systematically evaluated, especially between the species of <i>P. cruentum</i> and <i>P. purpureum</i>. The present study aimed to evaluate the production and fluorescence characteristics of phycoerythrin of three strains of <i>Porphyridium</i>. The results showed that <i>P. purpureum</i> SCS-02 presented the highest biomass, phycoerythrin content and yield were 6.43 g L<sup>−1</sup>, 9.18% DW and 0.288 g L<sup>−1</sup>, respectively. There was no significant difference between <i>P. purpureum</i> and <i>P. cruentum</i> in α and β subunits amino acid sequences of phycoerythrin and in fluorescence characteristics. The high gene expression level of the key enzymes in phycoerythrobilin synthesis (porphobilinogen synthase and oxygen-dependent coproporphyrinogen-III oxidase) could be related to the high phycoerythrin content of <i>Porphyridium</i>. Based on systematic evaluation, <i>P. purpureum</i> SCS-02 was selected due to its high biomass and phycoerythrin yield. <i>P. purpureum</i> and <i>P. cruentum</i> were highly similar in the phylogenetic tree, as well as in fluorescence characteristics; therefore, it was speculated that they might be the same <i>Porphyridium</i> species.
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