Different methods using rRNA secondary structure to assist phylogenetic analyses have been recently developed. In order to evaluate the structure information on accuracy of phylogenetic tree topology, comparisons of these methods were performed. Our results showed significant superiority of phylogenetic analyses incorporating secondary structure over the pure traditional approaches. When the three major factors, alignment method, evolutionary model and tree search algorithm, were considered simultaneously in phylogenetic analyses, the implementation of structure information in alignment and substitution model produced a noticeable positive effect on topological accuracy.