Abstract: The two non-coding chloroplast regions，trnL-trnF and accD-psaI of 26 accessions from 19 Pyrus L. species and two outgroup accessions from Malus Mill. were sequenced. Aligned lengths of these two regions were 927 bp and 944 bp，respectively. A total of 36 substitutions and 11 indels were obtained in the combined data. All of the indels were treated as single mutation events and coded as substitutions manually when conducting maximum parsimony and Neighbor Net（NN）analyses. Our results showed that the indels in these two cpDNA regions were reliable phylogenetic characters and increased phylogenetic resolution；Compared with trnL-trnF，accD-psaI evolves quicker，providing more information for the discovery of inter- and intra-specific relationships in Pyrus. The NN split network indicated that the poor resolution in the phylogenetic tree was partly caused by conflicting signals or by lack of sufficient informative site. In addition，maternal lineages of putative inter-specific hybrids were revealed.

Key words: Pyrus, trnL-trnF, accD-psaI, indel, phylogenetic relationship