Japanese dwarf bamboos are representative floristic elements that characterize the understory in Japan. They contain many putative hybrid taxa that cause difficulty in morphological classification and identification. The interspecific hybridization is undetectable by molecular analysis using chloroplast DNA (cpDNA) markers due to maternal inheritance. This study aimed to develop two nuclear DNA (nDNA) markers of flowering genes that enable to differentiate hybrid species.

Specimens of parental species and their putative hybrids were collected. Thirty-eight samples of Sasa nipponica and Sasamorpha borealis and 18 of S. kurilensis and S. senanensis were collected from the University of Tokyo Chichibu Forest (UTCF) and the University of Tokyo Hokkaido Forest (UTHF), respectively. Twelve external morphological traits were investigated and the putative hybrids from UTCF were identified as Sasaella hidaensis, which is a hybrid between Sasa and Pleioblastus. Most samples from UTHF were identified as S. cernua, which is a S. kurilensis - S. palmata complex.

Molecular analysis using the cpDNA gene, rbcL, did not detect any nucleotide variations, except one in genus Sasamorpha. Analysis of the nDNA genes, FT and LFY homologs, revealed that the FT detected nucleotide variations with insertions and deletions, whereas the LFY did not have interspecific variations although several heteroduplexes were detected.