A rice BAC library is being used widely in rice genome researches due to its distinctive advantages over other library systems. Physical locations of the rice bacterial blight resistance gene, Xa-5, was mapped comparatively with a BAC clone linked to this gene, in Oryza sativa, a cultivated rice and Oryza officinalis, a wild rice. Xa-5 was in situ hybridized to O. sativa and O. officinalis chromosomes. Xa-5 was located on the short arm of chromosome 5 in O. sativa but on the long arm of chromosome 5 in O.officinalis with fraction length (FL) 48.85 and 47.30%, respectively and their FL were consistent with the results obtained by using the selective marker of rice, RG556, as a probe. The frequencies of signal detection of the marker, RG556 and the BAC clone, 44B4, were 8.0 and 41.3% in O. sativa, while 9.0 and 42.3% in O. officinalis, respectively. Based on a comparative RFLP map of a wild rice, O. officinalis and O. sativa, comparative analyses of karyotypes of O. officinalis were demonstrated firstly by fluorescent in situ hybridization (FISH) using a BAC clone and an RFLP marker from O. sativa as probes.