Abstract:Genomic in situ hybridization (GISH) was used to detect the AA genome distribution of Eleusine indica (L.) Gaertn. on chromosomes of E. coracana (L.) Gaertn. (AABB), and the homoeologous relationship between AA and BB genomes was studied. The ultrasonic processor pre-sheared total DNA of E. indica further labeled by nick translation mix as probe and the sheared total DNA of E. floccifolia (Forssk.) Spreng. (BB) as blocking DNA, and then they were hybridized to the metaphase chromosomes of E. coracana. The results showed that the AA genome of E. indica was distributed in 18 chromosomes of E. coracana. When not adding or adding excess blocking DNA, the AA genome was not detected on the chromosomes of E. coracana, suggesting that the AA and BB genomes may have not yet been well differentiated from each other, and that E. indica and E. floccifolia may share abundant repeated sequences. The 300-750 bp fragment peaks were presented on the 1% agar gel after shearing total DNA of E. indica and E. floccifolia 2 min and 3 min, respectively. The difference in the time of DNA shearing of the two species suggests that the ultrasonic processor method should be adjusted depending on species in order to obtain DNA probes with appropriate lengths.