Considering the alarming prospect of at least two in five plant species facing extinction, it is urgent to identify unsecured phylogenetic branches within the plant Tree of Life and adopt appropriate conservation strategies. While conventional seed banking has the potential to safeguard a large part of world's flora, the scarcity of phylogenetically informed ex situ conservation programmes poses a challenge to effective plant conservation. Leveraging an extensive dataset of seed collections across 109 European seed banks, our study reveals that current collections capture a phylogenetically diverse subset of the European flora. However, they safeguard between 43.296.40 suggesting that specific major branches of the plant phylogeny in Europe remain unprotected. To address this gap, we introduce a novel quasi-deterministic method to generate a list of unbanked species, prioritized by evolutionary significance. Although this approach can enhance the evolutionary quality of seed bank collections, biological, technical and practical constraints may limit conventional seed banking for some of these priority species. We advocate for an enhanced coordination among conservation facilities and the integration of phylogenetic perspectives with advancements in ex situ conservation techniques beyond conventional seed banking, to effectively conserve plant evolutionary heritage.