Gene and genome duplications play a central role in plant evolution. Despite this, the role of gene copy number variations (CNVs) as a source of genetic variation that contributes to intra- and inter-species diversity and divergence in plants has been largely unaddressed. Here we present a microarray-based survey of CNVs between A. thaliana and two of its most closely related species, A. halleri and A. lyrata. To obtain primary data about the respective genomes, we successfully used the technique of cross-species comparative genome hybridization (CGH) on Affymetrix ATH1 GeneChips. We thus bypassed the limiting need for fully assembled genomes in such comparative studies. We report a significant enrichment of CNVs for metal homeostasis and metal transport genes in Arabidopsis halleri, a metal hypertolerant hyperaccumulator that inhabits highly metal-contaminated sites. We validate our results and address the limitations of our study by comparing against the recently published A. lyrata genome sequence. Our study is the first attempt to specifically characterize inter-specific CNVs in plants. The role of CNVs in plant adaptation to environmental constraints is highlighted by our findings.