The impact of man-made noise on wildlife is recognised as a major global concern affecting many taxa in both terrestrial and aquatic ecosystems, with the degree of impact varying among individuals or species. Understanding the factors inducing intra-species differences in response to noise is essential for the development of adapted and effective mitigation measures. This study compares the behavioural response of Cape fur seals to boat noise exposures at two study sites showing differences in their level of exposure to anthropogenic activities, and individual composition. Increased vigilance was found for Lambert's Bay seals exposed to high noise level (70-80 dB) compared to those tested at Cape Town harbour. Comparisons with a similar study performed in Namibia were made. Intrinsic factors such as individuals' age-class, sex or arousal state as well as extrinsic factors such as the ambient noise and the nature/extent of human-seal interactions were suggested to induce such variation.