Sea ice is a critical component of the Earth’s Climate System and a unique habitat. Sea-ice changes prior to the satellite era are poorly documented, and proxy methods are needed to constrain its past variability. Here, we demonstrate the potential of sedimentary DNA from Polarella glacialis, a sea-ice microalga, for tracing past sea-ice conditions. We quantified P. glacialis DNA (targeting the nuclear ribosomal ITS1 region) in Arctic marine and fjord surface sediments and a sediment core from northern Baffin Bay spanning 12,000 years. Sea ice and sediment trap samples confirmed that cysts of P. glacialis are common in first-year sea ice and sinking particulate matter following sea-ice melt. Its detection is more efficient with our molecular approach than standard micropaleontological methods. Given that the species inhabits coastal and marine environments in the Arctic and Antarctic, P. glacialis DNA has the potential to become a useful tool for circum-polar sea-ice reconstructions.