AbstractLarge‐scale evaluation of genetic diversity in crops with large and complex genomes benefits from the selective enrichment of relevant genomic regions prior to sequencing. Given the complexity of the sugarcane (Saccharum spp.) genome and the limited exploration of quantitative trait loci (QTL) for important energy traits, we used comparative genomics with the related diploid crop sorghum (Sorghum bicolor) to mine for regions associated with bioenergy production. Twenty‐one meta‐QTL (mQTL) were identified after surveying 286 QTL from 24 different studies using the Sorghum QTL Atlas. Comparative genomics revealed that at least 35% of genes located within QTL can be found in highly conserved sorghum/sugarcane collinear chromosome blocks. Additionally, a targeted candidate search identified 200 genes known for their involvement in sugar and cell wall metabolism. For a subset of these sorghum genes, we evaluated sugarcane gene copy number, sequence identity, and homoeolog expression in target tissues. This work is an initial step towards targeting and resequencing sugarcane orthologous genomic regions to discover single nucleotide polymorphisms (SNPs) as a resource for genomics‐assisted breeding.