Moraceae, with its seven tribes, 45 genera, and approximately 1,200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogeny of Moraceae species remains challenging due to their diverse morphological features. To address this issue, we sequenced seven complete plastomes and analyzed online datasets for other 42 species at the tribal level within Moraceae. Our analysis revealed that all the plastomes within this family had a typical quadripartite structure and ranged from 159,449 to 161,478 bp in length. Comparative plastome analyses revealed ten highly variable regions (ndhF-rpl32, rps4-trnT, rps15-ycf1, trnC-petN, ycf1, etc.). A total of 5,022 dispersed and tandem repeats along with 4,430 simple sequence repeats (SSRs), were identified, highlighting their potential for the development of molecular markers in Moraceae. While the evolutionary rates across the various tribes of Moraceae were found to be similar, the genes ndhK, ndhD, rps2, and rps12 displayed evidence of positive selection. Codon usage bias was shaped by mutation and selection, with significant natural selection observed on genes such as clpP, ndhC, ndhI, etc. Additionally, thirteen optimal codons were identified for 10 genes. This study confirms that the seven tribes within the Moraceae family are monophyletic, with divergence estimated to have occurred approximately 79.43 million years ago. This timing coincides with the formation of modern rainforests and a burst in angiosperm diversity towards the end of the Cretaceous period. Overall, our study provides a robust phylogeny and a temporal framework for further research on phylogeography and population genetics of Moraceae. Furthermore, our genomic resources will be available for genetic engineering and germplasm exploration within this versatile plant family.