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The AEFishBIT tri-axial accelerometer was externally attached to the operculum to assess the divergent activity and respiratory patterns of two marine farmed fish, the gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax). Analysis of raw data from exercised fish highlighted the large amplitude of operculum aperture and body tail movements in European sea bass, which were overall more stable at low-medium exercise intensity levels. Cosinor analysis in free-swimming fish (on-board data processing) highlighted a pronounced daily rhythmicity of locomotor activity and respiratory frequency in both gilthead sea bream and European sea bass. Acrophases of activity and respiration were coupled in gilthead sea bream, acting feeding time (once daily at 11:00 h) as a main synchronizing factor. By contrast, locomotor activity and respiratory frequency were out of phase in European sea bass with activity acrophase on early morning and respiration acrophase on the afternoon. The daily range of activity and respiration variation was also higher in European sea bass, probably as part of the adaptation of this fish species to act as a fast swimming predator. In any case, lower locomotor activity and enhanced respiration were associated with larger body weight in both fish species. This agrees with the notion that selection for fast growth in farming conditions is accompanied by a lower activity profile, which may favor an efficient feed conversion for growth purposes. Therefore, the use of behavioral monitoring is becoming a reliable and large-scale promising tool for selecting more efficient farmed fish, allowing researchers and farmers to establish stricter criteria of welfare for more sustainable and ethical fish production.