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In order to achieve certain targets of the Global Strategy for Plant Conservation (GSPC), countries should aim to have at least 75% of their threatened species preserved in ex situ genetically representative collections, preferably in the country of origin, and at least 20% of the threatened species must be available for recovery plans and restoration programs (Target 8). Assessing the conservation value of ex situ collections is needed in order to identify the gaps in gene banks and to determine the baseline situation. Selection of the target species for conservation followed the Regional Responsibility criterion, as the first-order of priority at the local level with highest ranking given to species whose distribution is endemic to the study area. Data analysis was performed on 85 species listed in the Valencian Catalog of Threatened Plant Species (VCTPS) stored in the Germplasm Bank Collections of Valencian Flora, Spain. Our results show that conservation value of an ex situ collection will depend on whether the analysis is based on the representation of species (i.e. the presence or absence of species in an ex situ collection) or based on their representativeness (i.e. how well the collected and stored natural populations represent the “theoretical” species genetic diversity and what is the potential to produce plants for recovery actions, summarized in the proposed index R4). For 85 species listed in VCTPS the existing ex situ seed bank collections keep samples of 91.8% (78 species), indicating good representation. However, the criteria accounting for number of populations collected and quality of the stored germplasm revealed that less than 50% of the listed species are properly preserved in the ex situ collections.