To help the analysis of our sperm transcriptomic data, we produced a new integrative S. aurata genome annotation using the RNAseq data from our experiments. This new annotation was carried out by re-annotating the available S. aurata reference genome and by adding 202 de novo assembled transcripts that were not present in the genome assembly. In total, 31,501 protein-coding genes were annotated, which produced 57,396 transcripts (1.82 transcripts per gene) and encoded for 51,365 unique protein products. Functional labels were assigned to 62% of the annotated proteins. In addition,165,898 non-coding transcripts were annotated, of which 159,925 are long non-coding RNA (lncRNA) genes and 5,973 correspond to short non-coding RNAs.