The Mugilidae family comprises several euryhaline species of significant ecological and economic value in global fisheries and aquaculture. Despite close taxonomic relationships, Chelon auratus, Chelon ramada and Mugil cephalus differ notably in physiological traits, seasonal energy allocation and tissue composition, influencing both ecological roles and commercial value. This study investigates the effect of seasonality on the fish flesh quality and metabolic gene expression of these three commercially important mullet species, collected from their natural habitat in Klisova Lagoon, Greece, by analyzing proximate composition (moisture, ash, protein, lipid), hepatosomatic index (HSI) and expression of lipid metabolism genes. M. cephalus showed lower protein and lipid content than C. ramada and C. auratus. In this context, expression of key lipid metabolism genes (fabp, pparg, cpt) reflected these differences not only between species but also revealed patterns which differed between examined tissues and seasons. Notably, this study provides the first characterization of these genes in the species examined. HSI data further indicated species-specific and seasonal strategies for energy storage. The results contribute to refining harvest timing strategies, enhancing post-harvest handling practices, in an effort to promote market differentiation and eventually to improve the economic viability of the mullet fishery sector.