Abstract The use of acoustic signals to communicate is widespread among marine mammals and vocalizations are involved in all their social interactions. Due to many factors, acoustic features of a species' vocalizations may differ among populations. The present study investigated both micro‐ and macro‐geographical variation in the vocalizations of Cape fur seal females, males, and pups. Acoustic measurements were performed on calls recorded at four South African and two Namibian sites (maximum range ~ 1,000 km). Comparisons among close sites in South Africa revealed no micro‐geographical variation (maximum range ~130 km) in females' and pups' vocalizations. Barks of subadult males had different features among sites, which may be explained mostly by the context of call production. At the macro‐geographical scale (South Africa vs. Namibia), all call types varied significantly among sites. Several extrinsic and intrinsic factors were suggested to drive such differences. For females' and pups' calls, differences might be explained by environmental factors, whereas for males' barks, behavioral differences are the most likely explanation for acoustic differences (breeding vs. resting sites). Such investigations help understand how acoustic communication in marine mammals is shaped by ecological drivers.