This study describes the effects on the skeletal phenotype of two pivotal factors, density and water volume, don the hatchery (larval) phase of gilthead seabream (Sparus aurata) larvae previoulsy described for two model species (Danio rerio and Oryzias latipes) and sub-adult (pre-ongrowing) gilthead seabream (Sparus aurata). The experimental trial was conducted using single conditions in a pilot study, starting with a total of 615,385 eggs from the same batch. Three densities (LD low density: 25 larvae/L; MD medium density: 125 larvae/L; and HD high density: 250 larvae/L) and two water volumes (500 and 1000 L) were tested from spawning up to 60 days post-hatching (dph) (average standard length: 1.79 cm; average dry weight: 27.11 mg). On the final samples, morphometric, anatomical, and histological data were collected for data pertinent to meristic counts and skeletal anomalies. The results (analyzed by means of multivariate analyses) indicated that the LD-reared larvae were significantly longer and heavier than HD-reared fish. Furthermore, LD-reared gilthead seabream exhibited a significant reduction in the frequency of individuals with anomalies of jaws, vertebral body shape, and vertebral arches than the MD and HD conditions, which is in agreement with previous experiments carried out on model species and gilthead seabream sub-adults.