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American lotus ( Nelumbo lutea Willd.) was an important food resource for native American people and continues to be a popular ornamental plant worldwide. However, its habitats have been suffering from destruction by both natural and human's activities. Little is known about the genetic diversity of this species. In this study, genetic diversity and structure of American lotus in North America were evaluated based on seven populations using 19 microsatellite markers. Sixty alleles were obtained from 19 loci in seven populations. The number of effective alleles ( N E = 1.18), Shannon's information index ( I = 0.17), expected heterozygosity ( H E = 0.11) indicated a low level of genetic diversity in populations. High level of genetic differentiation among populations was reflected by F ST = 0.81 and AMOVA analysis. UPGMA dendrogram and STRUCTURE analysis clustered the seven populations into two clusters or gene pools. Population of Ocheechobee Lake in Florida formed an independent cluster or gene pool and is separated from other populations. Populations from Ontario and Maryland likely originated from individuals surviving floods or were introduced not long ago from other places. Further study is necessary based on more extensive sampling from other distribution regions and countries to better understand genetic diversity of American lotus. [ABSTRACT FROM AUTHOR]