Despite the value of Chilean flora, 46% of the species, currently evaluated, are critically endangered or endangered, so ex situ conservation measures are key to their preservation. We analyzed the current state and conservation gaps of the native species preserved in the Seed Base Bank (SBB) of the Instituto de Investigaciones Agropecuarias (INIA), the main curator of Chile's plant genetic resources. Our analysis showed that 3,040 seed accessions of native species are preserved in the SBB, corresponding to 1,256 species, which represents 26.9% of the Chilean flora. The area with the largest number of accessions collected corresponds to the northern and central parts of the country, indicating that there has been a bias in terms of concentrating efforts on the continental regions and ignoring other important geographical regions of Chile, such as those located in the insular territory. A quarter of the threatened plants belonging to the Chilean flora are not currently conserved in the SBB, as they are vascular species without seeds, which cannot be protected in the long term under the traditional conditions of a seed bank. Additional collection and research efforts are required to increase the collection of native species in the SBB, especially threatened and endemic species.