Plants growing in similar climates with extensively overlapping distributions may exhibit similar phylogeographic patterns, due to similarities in range shifts during past climatic oscillations. We tested and exploited this expectation in a comparison of the evolutionary and demographic histories of two related and co-distributed species endemic to Japan – Rhododendron pentaphyllum and R. quinquefolium. Genetic variation in sequences of noncoding chloroplast DNA regions and hundreds of nuclear single nucleotide polymorphisms were used to investigate 191 individuals from 13 populations of R. pentaphyllum and 142 individuals from 10 populations of R. quinquefolium. We found that the two species were not each other’s closest relative and we found different times to the most recent common ancestor of extant populations based on both chloroplast DNA and nuclear SNPs. Rhododendron pentaphyllum exhibited higher genetic variation between populations than R. quinquefolium, while the two species had similar patterns of genetic divergence between regions with slightly different divergence times. These lines of evidence suggest that the similar ranges of the two species are the result of repeated range shifts since speciation during climatic oscillations.