The transcriptome of haploid germ cells and ejaculated spermatozoa from wild-type seabream (Sparus aurata) was compared by RNAseq. The data establish the molecular signature during spermatozoa differentiation and reveal the involvement of novel endocrine mechanisms during sperm maturation in the efferent duct. Overall design: Haploid germ cells were isolated from the testis by fluorescence-activated cell sorting, and ejaculated spermatozoa was collected from after a soft pressure to the abdominal area of the fish. Illumina libraries were constructed for 4 replicates for each of the two samples, and each replicate was a pool of 3 different fish.