<p>Hawthorn (<i>Crataegus</i> spp.) is a horticulturally significant plant with multifunctional value encompassing edible, medicinal, ornamental, and economic uses. Although China represents a primary center of hawthorn genetic diversity with abundant resources, the genetic diversity and DNA fingerprinting of these resources remain poorly characterized. In this study, genetic diversity, population structure, principal coordinate analysis and DNA fingerprints of 82 hawthorn accessions including 80 domestic accessions and 2 foreign accessions, were carried out using 22 polymorphic simple sequence repeat (SSR) markers. At the population level (observed alleles (Na) = 9.727, effective alleles (Ne) = 3.361, Shannon’s information index (I) = 1.426, observed heterozygosities (Ho) = 0.723, expected heterozygosities (He) = 0.671), the polymorphic information content (PIC) ranged from 0.304 to 0.815, with an average value of 0.623, demonstrating relatively high genetic diversity among these accessions. The combined values of the probability of identity (PI) and the probability of identity among siblings (PIsibs) across 22 SSR markers were 3.67 × 10⁻¹⁹ and 2.38 × 10⁻⁸, respectively, confirmed the strong discriminatory power of the SSR markers for fingerprinting. Cluster analysis, population structure and PCoA analysis collectively categorized these accessions into four major groups. Furthermore, the 82 accessions were fingerprinted using five core SSR primers. The results revealed differential discrimination capacities: primer Pr316 distinguished 19 accessions, whereas primers Pr224 and Pr454 resolved 14 and 13 accessions respectively. Here we present an analysis of the genetic diversity of hitherto unreported Chinese hawthorn germplasm and develop its DNA fingerprints through five core SSR markers, providing support for future resource conservation, development, and breeding efforts.</p>