Stressful events can alter organism physiology at several levels triggering allostatic responses. Telomeres are well-conserved repetitive DNA sequences mainly localised at chromosome's ends, playing a crucial role in DNA stability. Analyses of telomere dynamics are new tools to assess consequences of environmental stress in non-model organisms like fish. In this study, the relationship between freshwater tolerance and telomere dynamics was investigated in the gills of the European sea bass Dicentrarchus labrax. Fluorescent in situ hybridisation of telomeric sequences revealed distal telomeres as well as intrachromosomal telomeres known as interstitial telomere sequences. In order to better understand telomere dynamics in the gills of D. labrax, we used quantitative PCR to measure telomere length and mRNA expression of the catalytic subunit of telomerase reverse transcriptase tert. For the calculation of the relative telomere length, two reference genes were tested: the single copy gene mc2r, encoding melanocortin 2 receptor and the multicopy gene 18S, encoding the 18S ribosomal RNA. We proposed a novel normalisation method to calculate the relative telomere length using both, single and multiple copy genes as references. Cell dynamics was also investigated by measuring mRNA expression of genes involved in apoptosis (caspase 8 and 9), cell proliferation (proliferation cell nuclear antigen), aerobic mitochondrial metabolism (ATP citrate-synthase), anaerobic metabolism (lactate dehydrogenase a) and antioxidant enzymatic defences (superoxide dismutase 1 and 2, catalase). Following a 15-days fresh water exposure, telomere dynamics was not significantly modified in the gills of freshwater tolerant fish. But freshwater intolerant fish exhibited telomere attrition relative to saltwater controls, and lower expression of tert in gills relative to freshwater tolerant fish. This modification of telomere dynamics in intolerant individuals was found to be correlated with lower antioxidant enzymatic defences, a higher aerobic metabolic marker and a lower cellular turnover. These data bring new perspectives for the use of telomere dynamics as an integrative marker to study environmental stress in fish, while considering individual phenotypic plasticity in response to freshwater exposure.