The species within Orobanchaceae cover all forms of parasitism from full autotrophy to holoparasitism. Although parasitic species have gone through dramatic genome changes, the plastomes of land plants generally contain highly conserved structures. We investigated the complete plastome sequence of hemiparasitic Pedicularis ishidoyana, belonging to the largest genus in Orobanchaceae, and compared it with the highly rearranged genomes of other taxa in that family. This plastome comprises a total of 152 571 bp, with two inverted repeats (IRs) of 35 281 bp, a large single-copy region (LSC) of 81 982 bp, and an extremely reduced small single-copy (SSC) region of 27 bp. Although IR expansion and SSC contraction have been reported in the plastomes of other hemiparasitic species in Orobanchaceae, the IR region of P. ishidoyana is extremely expanded, resulting in a very small SSC region. This genome contains 101 genes that encode 67 proteins, four rRNAs, 30 tRNAs, and 22 duplicated genes in the IR region. In contrast to other hemi- or holoparasitic members of Orobanchaceae, genes in the ndh family in P. ishidoyana (except ndhE) have lost their function through pseudogenization (six genes) or deletion (four genes). Therefore, it seems that the degradation of this gene family in P. ishidoyana has occurred independently. Phylogenetic analysis, including all parasitic types, strongly supports the conclusion that P. ishidoyana diverged early from autotrophs and is sister to holoparasitic taxa. Our results suggest that these hemiparasitic Pedicularis plants might represent an early stage of parasitism that has developed stepwise in this family from non-parasites to holoparasites.