Plantago hakusanensis (2n = 4x = 24) is an endangered endemic species that occurs in subalpine zones in Japan. To clarify the unresolved taxonomic status of P. hakusanensis within the subgenus Plantago, we conducted a phylogenetic analysis based on the nuclear-encoded single-copy gene sucrose–proton symporter 1 (SUC1) using 60 previously reported alleles from 24 taxa in the subgenus Plantago. We found that P. hakusanensis was closely related to P. asiatica var. densiuscula. The phylogenetic relationships between P. hakusanensis and P. asiatica var. densiuscula were examined by analyses of the SUC1 nuclear regions and the internal transcribed spacer (ITS) of rDNA, genome-wide single-nucleotide polymorphism genotyping (via multiplexed inter-simple sequence repeat genotyping by sequencing), as well as additional analyses of three chloroplast (cp) regions (trnL-F, ndhF-rpl32, and rpl32-trnL) in 25 individuals of P. hakusanensis and 53 individuals of P. asiatica var. densiuscula. Monophyly of P. hakusanensis was suggested by the nuclear marker analyses, whereas the cp haplotypes of P. hakusanensis were shared with P. asiatica var. densiuscula and P. asiatica in China. The disparity between the nuclear and cp data may be explained by introgression of the cp genome (cp capture) during Quaternary climate changes. Our results provide (i) a molecular phylogenetic basis for the taxonomy and (ii) insight into the intraspecific diversification history of P. hakusanensis.