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The principle aim of this study is to elucidate the relationship between the fatty acid desaturase 2 gene (<i>fads2</i>) expression pattern in peripheral blood cells (PBCs) and liver of gilthead seabream (GSB), <i>Sparus aurata</i> broodstock in order to determine the possible use of <i>fads2</i> expression as a potential biomarker for the selection of broodstock. This selection could be utilized for breeding programs aiming to improve reproduction, health, and nutritional status. Passive Integrated Transponder (PIT)-tagged GSB broodstock (Male-1.22 ± 0.20 kg; 44.8 ± 2 cm and female-2.36 ± 0.64 kg; 55.1 cm) were fed a diet containing low levels of fish meal and fish oil (EPA 2.5; DHA 1.7 and n-3 LC-PUFA 4.6% TFA) for one month. After the feeding period, <i>fads2</i> expression in PBCs and liver of both male and female broodstock were highly significantly correlated (r = 0.89; <i>p</i> < 0.001). Additionally, in male broodstock, liver <i>fads2</i> expression was significantly correlated (<i>p</i> < 0.05) to liver contents in 16:0 (r = 0.95; <i>p</i> = 0.04) and total saturates (r = 0.97; <i>p</i> = 0.03) as well as to 20:3n–6/20:2n–6 (r = 0.98; <i>p</i> = 0.02) a Fads2 product/precursor ratio. Overall, we found a positive and significant correlation between <i>fads2</i> expression levels in the PBCs and liver of GSB broodstock. PBCs <i>fads2</i> expression levels indicate a strong potential for utilization as a non-invasive method to select animals having increased fatty acid bioconversion capability, better able to deal with diets free of fish meal and fish oil.