Centromeres are responsible for sister-chromatid cohesion, kinetochore formation, and accurate transmission of chromosomes. Rice provides an excellent model for organizational and functional studies of centromeres since several of its chromosomes contain limited amounts of satellite and other repetitive sequences in their centromeres. To facilitate molecular characterization of the centromeres, we screened several BIBAC and BAC libraries of japonica and indica rice, using several centromere-specific repeat elements as probes. The positive clones were identified, fingerprinted and integrated into our whole genome physical map databases of the two rice subspecies. BAC/BIBACbased physical maps were constructed for the centromeric regions of the subspecies. To determine whether the genomic organization of the centromeres has changed since the cultivated rice split from its progenitor and to identify the sequences potentially playing an important role in centromere functions, we constructed a large-insert BIBAC library for the wild progenitor of Asian cultivated rice, O. rufipogon. The library contains 24,192 clones, has an average insert size of 163 kb, and covers 5 x haploid genome of wild rice. We screened the wild rice library with two centromere 8-specific overgo probes designed from the sequences flanking centromere 8 of japonica rice. A BIBACbased map was constructed for wild rice centromere 8. Two of the clones, B43P04 and B15E04, were found to span the entire region of the wild rice centromere and thus selected for sequencing the centromere. By sequencing the B43P09 clone, a 95% genomic sequence of the long arm side of wild rice centromere 8 was obtained. Comparative analysis revealed that the centromeric regions of wild rice have a similar gene content to japonica rice, but the centromeric regions of japonica rice have undergone chromosomal rearrangements at both large scale and nucleotide levels. In addition, although the 155-bp satellite repeats showed dramatic changes at the middle region, they are conserved at the 5' and 3' ends of satellite monomers, suggesting that those regions might have important functional roles for centromeres. These results provide not only new insights into genomic organization and evolution, but also a platform for functional analysis of plant centromeres.