Celtis is a Cannabaceae genus of 60-70 species of trees, or rarely shrubs, commonly known as hack-berries. This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals. Although previous studies have identified its phylogenetic position, interspecific relationships within Celtis remain unclear. In this study, we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources. The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp, with a typical angiosperm quadri-partite structure, and encoded a total of 132 genes with 20 duplicated in the IRs. Comparative analyses showed that plastome content and structure were relatively conserved. Whole plastomes showed no signs of gene loss, translocations, inversions, or genome rearrangement. Six plastid hotspot regions (trnH-psbA, psbA-trnK, trnG-trnR, psbC-trnS, cemA-petA and rps8-rpl14), 4097 polymorphic nuclear SSRs, as well as 62 low or single-copy gene fragments were identified within Celtis. Moreover, the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C. biondii as sister to the ((((C. koraiensis, C. sinensis), C. tetrandra), C. julianae), C. cerasifera) clade. These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny, population genetics, and conservation biology.