Phalaris arundinacea L. (reed canary grass) is a widely occurring grass throughout the northern hemisphere. In north America it is thought to consist of introduced agricultural forms from Europe as well as native populations. It is likely that a \"cryptic invasion\" is progressing, with vigorous invasive biotypes ousting native occurrences, a process that is not readily recorded when the invader is conspecific with natives. We surveyed Phalaris arundinacea in western Canada using sequences of the internal transcribed spacer (ITS) of the nuclear ribosomal DNA. Two ITS ribotypes were discovered: one full length (ITS-long) and one with a seven base pair deletion (ITS-short). ITS-long plants are generally associated with anthropogenic or disturbed grassland habitats, often where commercial seed is likely to have been sown. ITS-short plants are more likely to be found in remote areas, in riparian and lacustrine habitats, and are thus candidates for native status. In addition, ITS-long plants have fixed heterozygosity indicating possible polyploidy. Phylogenetic analysis reveals that ITS-short is a unique mutation that characterizes an infraspecific clade. We designed an efficient PCR-based assay that allows sizing of a 238/245 base pair fragment in a capillary sequencer.