Selenium is an essential micronutrient for animals and humans, but can be toxic at higher levels. Manipulation of Se metabolism in plants may enable plants to be tailored to enhance Se content for human and animal consumption and to decontaminate Se polluted soils. Here, we generated subtracted cDNA libraries from perennial ryegrass roots and leaves, enriched for genes which expression is enhanced under toxic levels of selenium. The libraries were sequenced using next generation sequencing technologies to characterize the pool of enriched genes. Within these subtracted libraries, there were a large number of genes involved in the calcium-calmodulin signaling network. Furthermore, in the leaf subtracted cDNA library, we identified 28 ABC transporters. Subsequent expression analysis by quantitative RT-PCR demonstrated the significant accumulation of these transcripts in the leaf tissue of perennial ryegrass under toxic levels of Se. These results suggest a role for ABC transporters in selenium movement and accumulation in perennial ryegrass.