Gene flow between Dalmatian toadflax (DT) and yellow toadflax (YT), both aggressive invaders throughout the Intermountain West, is creating hybrid populations potentially more invasive than either parent species. To determine the direction of gene flow in these hybrid populations, species-diagnostic cytoplasmic markers were developed. Markers were based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) polymorphisms in the trnT-D chloroplast DNA (cpDNA) region digested with Alu1, and single-nucleotide polymorphisms (SNPs) in the matK and trnL-F chloroplast-barcoding regions. Four hybrid toadflax populations sampled from Colorado, Montana, and Washington contained both DT and YT cytoplasm, with YT predominating; 25 individuals from a fifth hybrid population from Idaho all had identical YT cpDNA haplotypes. Thirteen plants from two Colorado populations, assumed to be DT based on morphology and geographic isolation from any known YT population, were found to have YT cpDNA haplotypes. These results indicate that gene flow between invasive YT and DT populations is more widespread that previously realized and confirms that cryptic introgression of YT alleles has occurred in multiple western U.S. DT populations. The presence of YT genetic material in presumed DT populations may negatively affect host recognition and establishment by biocontrol agents used for toadflax management.