Plastomes, which are maternally inherited and show a moderate rate of evolution, play a critical role in phylogenetic reconstruction and assignment of plant species. However, little is known about the sequence divergence and molecular evolutionary patterns of plastid genomes in Elaeagnus mollis, a plant of great economic, medicinal, edible and ecological values. The plastid genome of E. mollis is 152,224-bp long and has 47 repeat sequences, including tandem (17), dispersed (12), and palindromic (18) types of repeat variations. Here, we reported six divergence hotspots (atpH-atpI, petN-psbM, trnT-psbD, trnP-psaJ, rpl32-trnL and ycf1) that could potentially be used as molecular genetic markers for population genetics and phylogenetic studies of E. mollis. A comparison of plastid genomes in the order Rosales showed that the trnH gene was duplicated only in Elaeagnaceae; therefore, it is an important marker in Elaeagnaceae. Phylogenetic analyses based on whole plastid genome sequences in 33 species revealed that Rosales is divided into two strongly supported clades and that the families Elaeagnaceae and Barbeyaceae are closely related.