Carnosine, a dipeptide composed of β-alanine and histidine, is predominantly found in animals such as mammals, birds, and fish, with no known presence in plants, microalgae, and other organisms. It can undergo methylation to produce anserine, β-alanyl-N-methyl-L-histidine. These imidazole peptides are known for their antioxidative properties and fatigue recovery effects. The synthesis of carnosine is catalyzed by carnosine synthase, encoded by the ATPGD1 or CARNS1 gene. Recently, homologous proteins to carnosine synthase have been reported from several microalgal genomes, although their biological functions remain unknown. In this study, we investigated the role of carnosine synthase-like protein in the green alga Monoraphidium braunii SAG 48.87. Initially, we examined the accumulation of carnosine and anserine in M. braunii cells cultivated under various conditions. Interestingly, salt stress induced the accumulation of anserine. The cells treated with 420 mM NaCl accumulated 38.3 μg g−1 dry weight (DW) of anserine. Expression of ATPGD1a, putatively annotated as a carnosine synthase gene, was induced under salt stress conditions, while expression of ATPGD1b was downregulated. The Escherichia coli cells expressing the recombinant ATPGD1a primarily accumulated anserine (269.9 μg g−1 DW) and a small amount of carnosine, although we could not confirm any carnosine or anserine synthesis by the purified recombinant protein. These findings suggest that the carnosine synthase homolog in microalgae may play a role in synthesizing imidazole dipeptides, and anserine could serve as a salt protective agent and help stabilize cellular functions, particularly under salt conditions. This is the first observation of the synthesis of the imidazole dipeptide from any organism except animals and anserine protecting from salt stress.