Technical Abstract: • Premise of Study: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that can serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze the genomic data for evidence of hybridization. • Methods: We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing data, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses. We also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. • Results: Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. • Conclusions: Transcriptome sequencing using next generation platforms has greatly reduced the cost of entry for genomic studies of non-model organisms, and the ESTs and microarrays reported here hopefully will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to quantify the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.