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Pseudogenes (Psi s), including processed and non-processed Psi s, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Psi s utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Psi s within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing similar to 28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Psi s on chromosomes showed a significantly negative correlation between Psi s/ORFs and their local gene densities, suggesting a higher proportion of Psi s in gene desert regions, e. g. near centromeres. On the other hand, compared with the non-Psi loci, even the intact coding sequences (CDSs) in the Psi loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Psi s mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.