This dataset supports the study "Does nutrients scarcity select for Synechococcus clade III in Mediterranean Sea?" It includes: (1) mesocosm experimental data (chlorophyll a, nutrient concentrations, Synechococcus abundance and growth rates); (2) rpoC1 amplicon sequencing-derived community composition; (3) reference genomes and the newly assembled genome of MSI/MSII isolated from Mediterranean Sea; (4) detailed information about the reference genomes and the newly assembled genome of MSI/MSII; (5) annotations and copy numbers of nitrogen/phosphorus transporters; (6) annotations and copy numbers of nitrogen/phosphorus metabolisms; (7) metatranscriptomic TPM values of nutrient transporter genes in ambient seawater. These data reveal that clade III outcompete other clades through superior nitrogen and phosphorus acquisition, multiple pstS copies, and active transporter expression under ultra‑oligotrophic conditions.