Natural hybridization between introduced species and their native congeners occurs frequently and can create serious conservation concerns. Ulmus pumila (Siberian elm) is an introduced Asian elm species that has naturalized in the United States and is now considered invasive in 41 states. Red elm (U. rubra), a native to the eastern United States, often occurs in sympatry with Siberian elm, and the two species are thought to hybridize. Here, we genetically characterized reference populations of the two elm species to identify species-specific microsatellite alleles. These markers were used to classify individuals in putative hybrid zones as parental species or hybrids, assess the extent of hybridization, and track patterns of introgression. We identified nine U. rubra, 32 U. pumila, and 51 hybrid individuals in our hybrid zones. Of the 51 hybrids, 35 were classified as first-generation hybrids and 16 as backcrosses. The majority of the backcrosses (88%) were introgressed toward U. pumila. Our classification of genotypes was consistent whether we used manual classification, principal coordinate analyses or Bayesian clustering. We observed greater genetic diversity and new combination of alleles in the hybrids. Our study indicates widespread hybridization between U. pumila and U. rubra and an asymmetric pattern of introgression toward U. pumila.