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Microalgae are photoautotrophic microorganisms known as producers of a large variety of metabolites. The taxonomic diversity of these microorganisms has been poorly explored. In this study, a newly isolated strain was identified based on the 18S rRNA encoding gene. The phylogenetic analysis showed that the isolated strain was affiliated with the <i>Rhodomonas</i> genus. This genus has greatly attracted scientific attention according to its capacity to produce a large variety of metabolites, including phycoerythrin. Growth and phycoerythrin production conditions were optimized using a Plackett–Burman design and response surface methodology. An expression profile analysis of the <i>cpeB</i> gene, encoding the beta subunit of phycoerythrin, was performed by qRT-PCR under standard and optimized culture conditions. The optimization process showed that maximum cell abundance was achieved under the following conditions: CaCl₂ = 2.1328 g/L, metal solution = 1 mL/L, pH = 7 and light intensity = 145 μmol photons/m²/s, whereas maximum phycoerythrin production level occurred when CaCl₂ = 1.8467 g/L, metal solution = 1 mL/L, pH = 7 and light intensity = 157 μmol/m²/s. In agreement, positive transcriptional regulation of the <i>cpeB</i> gene was demonstrated using qRT-PCR. This study showed the successful optimization of abiotic conditions for highest growth and phycoerythrin production, making <i>Rhodomonas</i> sp. suitable for several biotechnological applications.