Retrotransposons are ubiquitous components of plant genomes. They affect genome organization, and can also affect the expression patterns of neighboring genes. Retrotransposons are therefore important elements for changing genomic information. To understand the evolution of the Arabidopsis genome, we examined the distribution of certain retrotransposons, AtRE1s and AtRE2s, in the genomes of 12 natural variants (accessions) of Arabidopsis thaliana. AtRE1 and AtRE2 are copia-type retrotransposons that are potentially active. Their copy numbers are low, and they are absent from the genomes of some accessions. We detected four loci with AtRE1s inserted in six accessions, and one locus with an insertion of a solo-LTR-like sequence derived from AtRE1 in two accessions. Seven loci with AtRE2s inserted were detected on eight accessions. These loci were distributed in euchromatic regions of chromosomes 1, 2, 3, and 4. The AtRE1 and AtRE2 sequences at some loci identified in this study have not been recorded in the database of the 1001 Genome project. The sequences of AtRE1s and those of AtRE2s in different accessions and at different loci were highly conserved. There was a complete or almost complete conservation of sequences of both long terminal repeats in each AtRE1 and in each AtRE2. These results suggest that AtRE1 and AtRE2 appeared quite recently in the Arabidopsis genome. Furthermore, sequence comparisons of AtRE1 and AtRE2 loci among accessions revealed the possibility that large deletions containing entire sequences of AtRE1 and AtRE2 have occurred in some accessions.