In order to estimate synteny between A(t) and A polyploid wheat genomes belonging to different evolutionary lines (Timopheevi and Emmer), saturation of chromosome maps of Triticum timopheevii A(t) genome by molecular markers has been conducted. Totally, 179 EST-SSR and 48 genomic SSR-markers have been used with the following integration of 13 and 7 markers correspondingly into chromosome maps of A(t) genome. ESTSSR showed higher transferability and lower polymorphism than genomic SSR markers. The chromosome maps designed were compared to maps of homoeologous chromosome group of the T. aestivum A genome. No disturbances of colinearity, i.e., of the order of markers within the chromosome segments on which they had been previously mapped, were observed. According to the quantity assessment of markers amplifying in homoeologous chromosomes, the maximum divergence was detected in two groups (4A(t)/4A and 3A(t)/3A) among the seven chromosomes examined in the A (t) and A genomes. Comparison of molecular genetic mapping results with the published results of studying meiosis of F-1 hybrids and the frequency of chromosomes substitution in introgressive T. aestivum x T. timopheevii lines suggest that individual chromosomes of the A(t) and A genomes evolve differently. Translocations were shown to introduce the major impact on the divergence of 4A(t)/4A and 6A(t)/6A chromosomes, while mutations of the primary DNA structure, on the divergence of homoeologous group 3 chromosomes. The level of reorganization of other chromosomes during the evolution in the A(t) and A genomes was significantly lower.