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Spartina altemiflora (smooth cordgrass) has invaded Willapa Bay, Washington, covering bare mud flats and seagrass beds. At current expansion rates it threatens to occupy most of the intertidal habitat in the bay within 40 years. Although a major mitigation effort is underway, nothing is known about the genetic structure of the Willapa Bay S. altemiflora population or the underlying causes for the dramatic increase in seed set that has occurred in the last 15 years. Random amplified polymorphic DNA (RAPD) analysis was assessed as a method of DNA fingerprinting to analyse the genetic history and current structure of the Willapa population. The results suggest that all S. alterniflora clones in Willapa Bay are descended from a single genet. Given the limited genetic variability expected in a clonally founded population, we discuss the utility of RAPDs as genetic markers to explore the large morphological and reproductive differences reported among Willapa clones. Cluster analysis of RAPD fragments was used to show relatedness among S. alteniflora genets and may be helpful in locating the most prolific clones for mitigation efforts. Overall, RAPDs show great potential in genetic analysis of S. altemiflora, particularly in invasive populations where isozyme variability is low or nonexistent.

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