The phylogenetic relationships of Eriobotrya were examined based on cpDNA psbA-trnH and atpB-rbcL markers using 21 names with M. germanica, P. beauverdiana and R. indica as an outgroup. The results revealed that the sequencing analysis contained around 841 bp aligned DNA characters, where 81 bp were variables and 42 bp were informative polymorphic sites. Further analysis showed that the phylogeny tree divided the species of Eriobotrya into 4 clades. Eriobotrya bengalensis, E. bengaensis var. angustifolia and E. obovata were closely related and formed clade A. E. deflexa, E. fragrans and E. seguinii clustered into clade B. E. japonica, E. malipoensis and E. × daduheensis clustered into clade C and E. fusca, E. cavaleriei, E. tengyuehensis, E. condaoensis, E. serrata, E. hookeriana, E. petiolata, E. salwinensis and E. elliptica were clustered into clade D. The present study concluded that future research with more taxa and the use of more DNA barcoding markers may be needed to resolve the complete phylogeny and evolution of Eriobotrya.