Satellite magnetic anomaly maps show well-defined negative anomalies over some deep sedimentary marginal basins, such as the Nova Scotia marginal basin. A possible explanation would be the thermal demagnetization of the oceanic upper crust due to thermal blanketing by the sediments and the oceanic lower crust and uppermost mantle due to subsidence into hotter regions beneath. We examine this possibility by computing the thermoviscous remanent magnetization of the oceanic lithosphere beneath the Nova Scotia basin using a detailed thermal evolution model which takes into account the continental rifting, sea-floor spreading, and subsequent subsidence. It is concluded that the thermal demagnetization is not sufficient to explain the entire observed negative magnetic anomaly over the basin; it contributes ~40% to the anomaly. We suggest that a major part, ~60%, of the anomaly arises from the particular location of the early Mesozoic oceanic lithosphere beneath the basin, which has a relatively weaker bulk remanent magnetization compared with a highly magnetic continental crust in the west and north and the strong magnetic oceanic lithosphere of the Cretaceous Quiet Zone in the east.