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Extinction through hybridization can threaten endangered species when hybrids are vigorous and fertile. We studied hybridization between the endangered small white lady’s slipper (Cypripedium candidum Muhlenberg ex Willdenow) and the common yellow lady’s slipper (Cypripedium parviflorum Salisbury var. makasin (Farwell) Sheviak and C. parviflorum var. pubescens (Willdenow) O.W. Knight) in four Manitoban populations. We used 8 morphological characters and 1061 amplified fragment length polymorphism (AFLP) loci to characterize variation in 182 plants. Canonical correlation analysis indicated that morphology was highly predictive of genetic composition. Ordination analyses of morphological and genetic data, and Bayesian clustering analysis of the genetic data, all clearly distinguished the two parental species. The two varieties of C. parviflorum were morphologically divergent but occupied the same genetic cluster in both ordination and Bayesian analyses. Putative hybrids had considerable morphological overlap with parental species but were mostly genetically intermediate. Five of 79 individuals assigned to C. candidum and 15 of 71 individuals assigned to C. parviflorum had genetic profiles consistent with mixed ancestry. These results suggest that some introgression has occurred, but genetic assimilation of endangered C. candidum by the more common C. parviflorum does not seem imminent. The high local abundance of C. candidum may reduce its susceptibility to gene flow from C. parviflorum. [ABSTRACT FROM AUTHOR]