Compared to hexaploid common wheat (Triticum aestivum, 2n=6x=42, AABBDD), little is known about microsatellites and their nucleotide sequences in related diploid wheat species carrying the Au or Am genomes. We tried to amplify homoeologous microsatellites from Triticum urartu (2n=2x=14, AuAu) and Triticum monococcum (2n=2x=14, AmAm ) using 54 sets of PCR primers originally designed for the microsatellites of the A genome of common wheat, and found that 26 primer sets amplified microsatellite products in all seven accessions of T. urartu and all three accessions of T. monococcum. On the basis of the amplification results, the nucleotide sequences of three representative homoeologous microsatellites were amplified from multiple accessions of T. urartu and T. monococcum and compared. The results showed that homoeologous microsatellites from T. urartu and T. monococcum varied in their nucleotide sequences. The patterns of nucleotide sequence variations differed among individual loci, with some showing variations only in the repeat regions or the flanking sequences and others in both the repeat regions and the flanking sequences. Nucleotide sequence variations in the flanking regions were caused by base substitution and/or indel mutations. The variations in the repeat regions involved changes in the repeat number or a combination of repeat number changes and insertions of additional types of dinucleotide sequences.