The emperor penguin, an iconic species threatened by projected sea-ice loss in Antarctica, has long been considered to forage at the fast ice edge, presumably relying on large/yearly-persistent polynyas as their main foraging habitat during the breeding season. Using newly developed fine-scale sea-icescape data and historical penguin tracking data, this study for the first time suggests the importance of less-recognized small openings, including cracks, flaw leads and ephemeral short-term polynyas, as foraging habitats for emperor penguins. The tracking data retrieved from 47 emperor penguins in two different colonies in East Antarctica suggest that those penguins spent 23% of their time in ephemeral polynyas and did not use the large/yearly-persistent, well-studied polynyas, even they occur much more regularly with predictable locations. These findings challenge our previous understanding of emperor penguin breeding habitats, highlighting the need for incorporating fine-scale seascape features when assessing the population persistence in a rapidly changing polar environment.