The quest for a renewable and inexpensive source of energy is one of the greatest challenges of the 21st century. Plants have already been used as a renewable source of energy, and continue to be one of the greatest hopes in this area. In order for plants to continue providing a cost-effective and renewable source of energy, it is imperative that their biomass growth and quality be constantly improved. Recent advances in the genomics field, led by the development of high-throughput sequencing and genotyping platforms, have opened up new strategies for accelerating plant breeding and aiding biotechnology development. Analyses of the vast amount of data generated by these modern genomics platforms are only possible with the constant development of computers and bioinformatics tools. In this chapter, we will present the genomic resources available for the most important plant species with bioenergy potential. Bioinformatics tools for gene expression analyses with RNA-Seq and for SNP genotyping are also presented.