Fish stress is a major concern in the aquaculture industry. Many stressors coming from routine practices can predispose fish to compromised growth, immunity and overall health. This study focuses on the characterization of the skin microbiota using next generation sequencing (NGS) platform by targeting a genomic marker 16S and to determine growth performance and immune status of gilthead seabream (Sparus aurata) during an episode of chronic stress. Two groups were established: control group and chronically stressed group. Stressed fish were subjected to 1 min air exposure twice a week for 4 weeks. Results showed that stress negatively affected fish growth performance. Cellular and humoral systemic immunity remained unaffected while local immunity in skin was positively stimulated (total IgM and peroxidase). Skin mucus microbial composition showed significant differences especially after 14 days. Stressed fish showed a decrease in the abundance of the genera Acinetobacter, NS3a_marine_group and Pseudomonas, while Pseudoalteromonas and Marinagarivorans increased significantly. In conclusion, air exposure stress was associated with alterations in skin mucosal immunity and microbial composition that may have been beneficial to the host favoring adaptation to stress.