Abastract: Studies on the secondary structures of rRNAs and adjacent regions has been considered as an important tool for inferring phylogenetic relationships at some taxonomic levels. Based on molecular clone , sequencing and secondary structure analysis on nrDNA ITS region in Nothotsuga longibracteata by the principle of minimizing free energy, structural characteristics were studied. Moreover, we discussed the structural differences between pseudogenic copy and functional copies. The results showed as follows: (1) the secondary structure of ITS1 is dominated by several extended haipins, with paired subrepeats partially overlapping at the conserved motif unique for Pinaceae, while unpaired subrepeats being fold onto itself and leaving part of the conserved motif exposed in hairpin loops; (2) the free energy value of pseudogenic copy is often higher than that of functional copy; （3）Compared with functional copies, the pseudogenic copy has more variable sites in the 5.8S region, which is symbolized by slow evolution rate, and has no contact sites in the 3' end with 26S ribosomal RNA.