Random Amplified Polymorphic DNA (RAPD) markers were used to determine whether populations of the global rarity Scirpus longii (Long's bulrush) are vulnerable to loss by introgression of genetic material from the weedy S. cyperinus (woolgrass). Shoots from 104 Scirpus plants were obtained from 10 sites in the watershed of the lower Medway River in Nova Scotia, Canada. A putative site of introgression (a seasonally flooded bog) was divided into five subsites: one large stand of vegetative plants and four patches of annually flowering plants clustered at one end of the site. Thirty-five dominant DNA markers were found among individuals from all sites and eight species-specific markers were identified for each of the two species. Nineteen different combinations of species-specific markers were present in the 39 individuals from the site of introgression, and, as expected for introgression, there was strong correlation (r  =  −0.80, p < 0.0001) between the numbers of the two types of markers. The vegetative and flowering subsites had distinctive hybrid indices: 0.76 and 0.27 of S. longii genome, respectively. The former indicates that S. cyperinus contributed about one-quarter of the genetic material of the plants from the subsite that accounts for more than 99% of the Scirpus at the site of introgression. Hybrid indices also show evidence of introgression in two of the 12 plants obtained at one of the presumed S. longii sites. Our results indicate that gene flow has occurred between S. cyperinus and S. longii at two S. longii populations, hybrid plants are capable of sexual reproduction, and Long's bulrush in Nova Scotia is vulnerable to loss by introgression. Conservation at the landscape level is needed to suppress anthropogenic disturbances that might allow S. cyperinus to threaten the genetic integrity of S. longii.