The worldwide decline of ocean fisheries stocks has provided a rapid growth in fish farming and the problems connected to animal welfare in aquaculture gained importance. In this context, we have looked for molecular markers among those genes whose expression could reasonably result modified by the different farming conditions. With this purpose, we have evaluated, in liver and brain of sea basses, grown for 3 months at different biomass density (<10, 80 and 100 kg/m3), the expression of those genes coding for proteins related to stress such as Heat Shock Proteins (HSPs), Metallothioneins (MTs) and Cytochrome P4501A (CYP4501A). In liver, the expression of MT and CYP4501A mRNA resulted induced in animals reared at 80 and 100 kg/m3. Inducible HSP70 appeared significantly over expressed only at the biomass of 100 kg/m3, while apparently, no induction was detectable for HSP90. In brain tissue instead, MT and HSP90 were induced already at 80 kg/m3; CYP4501A and HSP70 were influenced only at the higher population density of 100 kg/m3. In the last three decades, there has been an exponential increase in the interest concerning the description, classification and functional significance of stress-related proteins, in particular HSPs. These proteins represent precious biomarkers to evaluate the welfare conditions when they are still recoverable; detecting their mRNA by PCR is fast, easy and relatively inexpensive. Therefore, we propose this method as a good alternative to monitor fish welfare.