The aquatic plant species Egeria densa (Planch.) Casp and E. najas Planchon occur naturally in the Paraná River Basin of southeastern Brazil. Hydroelectric dam construction in the river basin has created several lakes, changing the ecology of the river and altering the population ecology of Egeria. Large, dense populations of Egeria now grow in Jupiá Lake and its tributaries, occasionally blocking hydroelectric turbines. This study is part of a larger project examining environmental changes associated with large dam projects; the research objective of this study was to assess patterns of genetic diversity in Egeria populations growing in Jupiá and Três Irmãos Lakes and their Paraná River tributaries using genetic markers. Forty-two plants of E. najas and 46 of E. densa (for a total of 88 samples) were collected from 13 sites. Genotypes were identified by isoenzymes and Random Amplification of Polymorphic DNA RAPD markers. Using a genetic distance dendrogram we grouped all E. densa plants into one set and all E. najas plants into another set. The plant sample 8a, which presented intermediary morphological characteristics of both species, also presented intermediary genetic characteristics, indicating the possibility that gene introgression between these Egeria species may occur. The creation of Três Irmãos Lake appears to have increased some measures of genetic diversity in Egeria populations by facilitating outcrossing among previously semi-isolated genotypes. Increased migration of large numbers of seeds and vegetative branches of E. densa and E. najas into Jupiá Lake and its tributaries can account for most of the changes in patterning of genetic diversity observed in these populations of Egeria.