<p>This study investigated the effects of dietary supplementation with <i>Synechococcus elongatus</i> PCC 7942 on the intestinal microbiota of zebrafish (<i>Danio rerio</i>). Using metataxonomic analysis based on 16S rRNA gene sequencing, the impact of supplementation on microbial composition and diversity was assessed. Results revealed that the intestinal microbiota remained generally stable, with no significant changes in alpha (Shannon and Simpson) or beta (Bray–Curtis) diversity indices, suggesting that supplementation did not compromise overall microbial health. Despite this general stability, a significant reduction in the relative abundance of the genus <i>Pirellula</i> was observed in the treated group. This genus, belonging to the Planctomycetota, is associated with the degradation of complex organic compounds, and its decline may indicate specific interactions between <i>S. elongatus</i> metabolites and the basal microbiota. Additionally, micoplasmas were exclusively detected in control samples, suggesting that supplementation may have created an intestinal environment less conducive to colonization by these opportunistic microorganisms. Another relevant factor was the dietary context, as the feed used included <i>Arthrospira platensis</i>, known to promote microbial stability. This likely contributed to the resilience of the microbiota, mitigating the effects of new interventions. The absence of dysbiosis and the selective metabolic impact of <i>S. elongatus</i> highlight its potential as a safe and functional dietary supplement in aquaculture.</p>