This study aimed at the indentification of the species and genotypes of the genus Crataegus in Syria and determination of the genetic relationships among them based on the analysis of genomic and chloroplast DNA (cpDNA) using ISSRs and CAPS techniques. Morphological characterization carried out on 49 Crataegus samples collected from different geographical regions of Syria revealed four Crataegus species: C. monogyna, C. sinaica, C. aronia and C. azarolus. In the dendrogram constructed for those samples based on ISSRs (20 primers), all samples that belong to C. monogyna were clustered in one cluster. Samples of the other three species were overlaped in another cluster. Two samples of these were the most distant from all other samples in the dendrogram and were suggested to represent hybrid species or subspecies. When CAPS technique was applied on four Crataegus samples that represent the four suggested species using 22 cpDNA regions and 90 endonucleases, no polymorphism was detected neither in amplification products sizes nor in restriction profiles. The inability of detection of variation in cpDNA among species suggested can be attributed to the low level of evolution of the cpDNA in the genus, and to the possibility that some of these species are either subspecies or hybrids since the cpDNA is inherited through one parent only.