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Manual acoustic telemetry was used to describe core habitat use of white sharks in the complex marine landscape of the Dyer Island and Geyser Rock system near Gansbaai, South Africa. We compared home range estimates and swimming pattern analyses to those established at Mossel Bay, another white shark aggregation area roughly 300 km to the east. Traditional home range estimates used in Mossel Bay did not account for movement or barriers, and were thus biased towards areas with very little shark movement (i.e. potential resting areas). We found that adapting a Movement-based Kernel Density Estimate (MKDE) could account for movement and barriers, resolving these issues. At Dyer Island and Geyser Rock, daytime shark habitat use was adjacent to the seal colony, with low rates of movement, non-linear swimming patterns and small activity areas. At night, rates of movement and linearity increased as sharks travelled further from the islands into deeper waters. MKDEs revealed 4 focal areas of habitat use: a channel between the 2 islands, an area to the south of the seal colony, another area near a kelp feature to the southwest of the seal colony and a reef system to the northwest. These results differed significantly from the habitat use at Mossel Bay, where focal areas occurred adjacent to the seal colony during the hours of dawn and dusk. We discuss possible explanations for these differences. This study is the first to make use of MKDEs in a complex marine landscape and highlights important differences in habitat use of a threatened species between 2 separate aggregation areas.