The objective of this study was to evaluate the genetic diversity and population structure of natural subpopulations of Paspalum rawitscheri (Parodi) Chase ex G.H. Rua & Valls using inter-simple sequence repeat (ISSR) molecular markers. Four natural subpopulations from State of Rio Grande do Sul, Brazil, were evaluated, using six ISSR primers. A total of 131 fragments were amplified, 34 of which were polymorphic. The genetic diversity (h) for the subpopulations was considered low, with values ranging from 0.130 to 0.217. The Vacaria subpopulation presented the lowest diversity among populations. The Shannon (I) diversity indices were also low, with values ranging from 0.187 to 0.334, with the Vacaria subpopulation also presenting the lowest values. The molecular variance (AMOVA) analysis showed, in general, the highest variation occurred within subpopulations rather than between subpopulations. The Bayesian Inference analysis separated the individuals into four genetic clusters, mixing individuals from different municipalities in the clusters. The results indicate that the species has low genetic diversity and low population structure, requiring conservation plans. Ex situ conservation becomes a necessary effort, since populations of this species are found in grasslands remnants affected by fires and implantation of crops, and is not present in any protected area of the Brazilian Conservation Units system.
