Degenerated oligonucleotide primerswere used to amplify, clone, and analyze sequence heterogeneity and chromosomaldistribution of 23 PCR fragments corresponding to the reverse transcriptase domain of copia-like retrotransposonsin rice. Of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were dividedinto 6 groups according to the phylogenetic and Southern blot analyses. Amino acid sequence differences among the22 aligned fragments ranged from 1 to 64%. Southern blot analysis of 10 rice accessions including indica, japonicaand common wild rice, using these 23 fragments as probes, showed that copia-like retrotransposons were presentin moderate to high copy numbers in all the rice genome although the exact copy number cannot be determined.The major difference revealed by southern analysis is a differentiation between the four indica varieties as onegroup and the four japonica varieties and the two wild rice accessions as another group. Polymorphisms were alsodetected among the indica and japonica varieties by major bands and repeatable minor bands. Five hybridizationbands were mapped to chromosomes 3, 4, 8, and 9, respectively. All the five bands were inherited in a dominantMendelian fashion and were not allelic with each other, indicating that the same element did not reside on the samelocation in different rice accessions. No transcript of the copia-like reverse transcriptase was detected on northernblot. The results suggest that the sequence heterogeneity and distributional variability of retrotransposons may beone of contributory factors causing genetic diversity in rice.