We used 22 fragments corresponding to thereverse transcriptase domain of copia-like retrotransposonsas representatives to study the organization and distributionof these elements in the rice genome. The loci detected by these22 fragments were assigned to 47 locations in the molecularlinkagemap involving all 12 chromosomes. The distributionalfeatures of copia-like retrotransposons found in the ricegenome indicated that (i) the loci detected were located mainlyin one arm of each chromosome; (ii) one fragment usuallydetected several loci that were mapped to similar locations ofdifferent chromosomes; (iii) retrotransposons sharing highidentity in nucleotide sequences were usually assigned tosimilar locations of the chromosomes; and (iv) concurrencesof multiple loci, detected by different fragments, in similarlocations or stretches of different chromosomes were commonin the rice genome. We also determined that the copy numberof copia-like retrotransposons in rice genome may be as low as'100 per haploid genome. The restricted distribution, alongwith low copy number, suggested that copia-like retrotransposonsin rice were relatively inactive during evolution comparedwith those in other plants. The distributional featuresof the copia-like retrotransposons suggested the existence ofpossible lineages among the rice chromosomes, which in turnsuggested that chromosome duplication and diversificationmay be a mechanism for the origin and evolution of the ricechromosomes. The information provided by fine mapping ofthe retroelements in the genetic linkage map may also beuseful for gene tagging and molecular cloning.