The scale and economy of next-generation sequencing is greatly improving researchers' ability to investigate organellar genomes. Here, we assemble and analyze the organellar genomes of taxa in monocots Asparagales and Poaceae. Genome size and the percent plastome were assessed in relation to percent coverage of final assemblies from total genomic DNA and isolated mitochondrial DNA. We found that shallow Illumina genome survey sequencing (GSS) data could be assembled and aligned to detect variation among organellar genomes, as well as rDNA loci. Data from chloroplast, mitochondrial, and rDNA loci can be used to build phylogenetic trees at much higher resolution and similar cost to traditional DNA barcoding methods.