Hawthorn (Crataegus spp.) is a wild fruit tree of considerable ecological, nutritional, and medicinal value, widely distributed throughout the Mediterranean region and other temperate areas. Its taxonomy is particularly complex due to high morphological variability and frequent synonymy, which complicates accurate species identification. In Algeria, Crataegus spp. are very common, exhibiting substantial variability, especially in the northern part of the country. Despite its broad distribution, information on the genetic diversity of Algerian hawthorn germplasm remains limited. Characterization of this diversity is essential to support the identification of valuable traits of interest and to provide suitable genetic resources for the effective valorization and conservation of the species. In this study, 205 samples of Algerian wild hawthorn were characterized through an integrated analysis based on morphological descriptors and SSR markers, separating the samples into two well-defined genetic groups corresponding to C. azarolus (CA) and C. monogyna (CM) species. High levels of allelic richness, heterozygosity, and private alleles revealed substantial genetic diversity within both species. Overall, the integration of morphological and molecular data will provide a valuable basis for the conservation and management of Algerian hawthorn genetic resources.