Four non-coding chloroplast region, trnL intron, trnT-trnL, trnS-psbC and accD-psaI were used to assay genetic diversity and phylogenetics of 88 pear accessions from Hubei Province. A totle of 11 variation sites included 6 SNP sites and 5 indel sites were recognized. Among 4 cpDNA regions, accD-psaI exhibited highest polymorphism with the most number of variable site, the most abundant haplotype diversity and nucleotide diversity. The values of nucleotide diversity and haplotype diversity of pear accessions in this study identified by four combined cpDNA fragments are 0.00112 and 0.769, respectively. All Tajima's D values are not statistical significant in P > 0.10, which indicate that variation of those chloroplast regions are based on natural theory of molecular evolution. A total of ten haplotypes are detected by the four cpDNA regions merging analysis. Among 13 collection sites, Jingmen and Xingshan own the most haplotypes. Hap2 and Hap5 are the two major haplotypes, which accounted for 31.82% and 30.68% of the total accessions, respectively. The network analysis of Pyrus L. cpDNA sequences showed that P. communis L. can be completely separated from oriental pear, and the rare haplotype Hap8 and Hap9 are all located in Jingmen, suggesting that the area may be one of the centers of origin or diversity of Pyrus L..