Background Allopolyploid speciation is a major evolutionary process in wheat (Triticum spp.) and the related Aegilops species. The generation of synthetic polyploids by interspecific crosses artificially reproduces the allopolyploidization of wheat and its relatives. These synthetic polyploids allow breeders to introduce agriculturally important traits into durum and common wheat cultivars. This study aimed to evaluate genetic and phenotypic diversity in wild einkorn (Triticum monococcum ssp. aegilopoides) accessions, to generate a set of synthetic hexaploid lines containing the various Am genomes from wild einkorn, and to reveal their agronomic characteristics.Results We examined the genetic diversity of 43 wild einkorn accessions using simple sequence repeat markers covering all the chromosomes and revealed two genetically divergent lineages, L1 and L2. The genetic divergence between these lineages was linked to their phenotypic divergence and the climate of their habitats. L1 accessions were characterized by early flowering, fewer spikes, large spikelets, and low-density spikelets compared to L2 accessions. These trait differences could have resulted from adaptation to their different habitats. We then developed 42 synthetic lines containing the AABBAmAm genome through interspecific crosses between T. turgidum cv. Langdon (AABB genome) as the female parent and the wild einkorn accessions (AmAm genome) as the male parents. Two of the 42 AABBAmAm synthetic lines exhibited hybrid dwarfism. Phenotypic variation, especially for days to flowering and spikelet-related traits, in the synthetic lines was significantly correlated with that in their wild einkorn parents. The phenotypic divergence between L1 and L2 accessions also reflected phenotypic differences among the synthetic lines. Furthermore, the AABBAmAm synthetic lines had longer spikelets and grains, long awns, high plant heights, soft grains, and late flowering, which are distinct from other synthetic hexaploid wheat lines such as AABBAA and AABBDD. Conclusions Wild einkorn genetically and phenotypically diverged into two lineages. The phenotypic variations in the synthetic lines reflected the divergence among wild einkorn. Utilization of various Am genomes of wild einkorn resulted in wide phenotypic diversity in the AABBAmAm synthetic hexaploids and provides promising new breeding materials for wheat.