Antarctic sea-ice plays a primary role in the climate system, potentially modulating interhemispheric millennial-scale climate change and deglacial warming. Recently, microfossil proxy data have provided important insights into this potential forcing. However, additional proxies for glacial sea-ice reconstructions are required, to support the microfossil data and to control for potential preservation issues. We considered highly branched isoprenoids (HBIs) as a sea-ice proxy, building on earlier studies in the Arctic and Antarctic. This study focused on measuring HBIs in glacial deposits in Southern Ocean deep ocean sediment cores. These deep ocean sites provided a study location away from the local sea-ice complexities associated with coastal and shallow water sites and allowed the comparison of HBIs during several phases of glacial sea-ice variability inferred from microfossils. Down-core profiles of di- and tri-unsaturated HBI isomers diene II and triene III were compared with diatom-based reconstructions of Antarctic sea-ice derived in three high resolution sediment cores recovered from a transect across the Scotia Sea, Southwest Atlantic. High quality chronological control was achieved through a combination of abundance stratigraphy, relative geomagnetic palaeointensity data, and down-core magnetic susceptibility/ice core dust correlation. Significant positive correlations, observed between HBI diene II and sea-ice presence, and between HBI triene III and open waters in the Marginal Ice Zone indicated that the two HBIs are both closely related to sea-ice and sea-ice edge dynamics, respectively. Highly significant down-core correlations between the HBIs indicate coeval sedimentation related to the summer breakdown of sea-ice melt-induced stratification. Combined, the two HBIs and diatoms demonstrated their potential as proxies for permanent sea-ice cover and sea-ice seasonality, two parameters poorly resolved in current climate models. The sea-ice reconstructions presented have developed our knowledge regarding HBIs and their relationship with the surface ocean environment and further highlight their potential as an important proxy for glacial Antarctic sea-ice and sea-ice dynamics back to at least ∼60 ka.