Soybean lecithin (SBL), used as a phospholipid source in larval fish diets, may compromise growth and survival in marine species, and affect gene expression, due to differences in fatty acid composition relative to marine lecithins (ML). The potential of SBL as a phospholipid source in gilthead seabream microdiets as compared to ML was evaluated. Two stocking densities were tested in order to exacerbate possible dietary effects: 5 and 20 larvae L(-1). Larvae reflected dietary fatty acid profiles: linoleic acid was higher, whereas eicosapentaenoic and arachidonic acids were lower in SBL fed groups than in ML fed larvae. Highest stocking density decreased survival, and led to elevated saturates and lower docosahexaenoic acid levels in polar lipid. Muscle histology observations showed hindered growth potential in SBL fed larvae. Despite similar cortisol levels between treatments, higher glucocorticoid receptor (GR), as well as hormone-sensitive lipase (HSL) mRNA levels in SBL fed groups revealed a role for fatty acids in gene regulation. Further analysed genes suggested these effects were independent from the hypothalamus-pituitary-interrenal axis control and the endocannabinoid system. Cyclooxygenase-2 and gluconeogenesis seemed unaffected. For the first time in fish, a link between dietary lecithin nature and HSL gene transcription, perhaps regulated through GR fatty acid-induced activation, is suggested. Enhanced lipolytic activity could partly explain lower growth in marine fish larvae when dietary ML is not provided.