Understanding the extent to which genetic diversity of wild populations in ex situ conservation can be retained is crucial for the management of such populations. Wild individuals collected in the target area in the past and present can be used to estimate the number of alleles lost over time in wild populations and thereby the number of alleles whose loss could be prevented by ex situ conservation. Here, we assessed the genetic diversity of wild and ex situ conservation populations of three endangered coastal herb species, Cirsium maritimum Makino (Asteraceae), Linaria japonica Miq. (Plantaginaceae) and Suaeda glauca (Bunge) Bunge (Amaranthaceae), which are endangered species on Awaji Island, Hyogo Prefecture, Japan, via multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). We incorporated the museomics approach, which involves conducting genetic analyses of museum specimens collected from the targeted wild populations in the past to estimate the temporal transition of genetic diversity in wild populations and the number of alleles maintained in ex situ conservation. Our results reveal a declining trend in genetic diversity in the wild populations of all investigated species, although this trend is not significant. In all the species, numerous alleles were already lost in current wild populations, whereas they were present in the past wild and ex situ conservation populations. Our study indicates that extinct alleles in current wild populations have been maintained in ex situ conservation by museomics approach. These approaches were effective in verifying the genetic diversity retention effects of ex situ conservation populations.