A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. ITS2 genetic distances were estimated comparatively by using both conventional DNA substitution models and RNA-specific models, which were performed in the PHASE package. Our results showed that the existence of the CBC substitution inflated the ITS2 genetic distances to different extents, and the deviation could be 180% higher if the relative ratio of substitution rate in ITS2 secondary structure stems was threefold higher than that in the loops. However, the CBC effect was minor if that ratio was below two, indicating that the DNA model is still applicable in recent lineages in which few CBCs occur. We thus provide a general empirical threshold to take account of CBC before ITS2 phylogenetic analyses.