The recent recognition of the five-subgenera classification within Crataegus has prompted discussion about the maternal phylogenetic relationships among these subgenera, with inconsistencies in taxon sampling, marker selection, and inference methods contributing to differing interpretations. In this study, we performed deep genome skimming sequencing and assembled 63 whole plastomes, including 58 from Crataegus and five from related genera as the outgroups. We employed multiple phylogenetic inference methods (Maximum Likelihood and Bayesian Inference) to reconstruct an accurate phylogeny. The whole plastome-based, maternally inherited trees consistently supported two major clades within Crataegus: one comprising C. subg. Crataegus and C. subg. Brevispinae, the other encompassing the remaining three subgenera. Within the latter clade, C. subg. Sanguineae and C. subg. Americanae formed a sister group, which together were sister to C. subg. Mespilus. Our analysis also revealed a close maternal relationship between C. shandongensis and C. pinnatifida var. major, suggesting the shared maternal ancestry. Furthermore, we updated the description of C. shandongensis based on extensive specimen examination and designated the lectotype for this species. This comprehensive taxonomic synopsis, supported by both phylogenomic and morphological analyses, provides a robust foundation for future taxonomic and evolutionary studies of the Shandong hawthorn.