A detailed study of the Turkish endemic Gypsophila pilulifera were presented by both morphological and molecular investigations of several sites (each one divided in four biotopes). The characteristics were investigated using statistic analyses, i.e. t-Test and One-way ANOVA tests, as well as Discriminant analysis (á=0.05). Some differences were detected among the individuals in the locations stufied where the species was distributed in terms of morphological characteristics and obvious similarities/differences were determined among the biotopes as a result of the discriminant analysis. Morphological characterization was supported by molecular data. Four individuals from two different locations were analyzed by PCR using twenty-four ISSR primers. Analysis of PCR products on agarose gel yielded three primary reproductive band profiles, and the similarity frequencies calculated with the Jaccard coefficient were found to be among 0.229 and 0.769. In this context, according to the results, there was no difference in species, subspecies or variety level between individuals between the two locations. But the obtained molecular differences support the morphological differences. It is predicted that this may change towards speciation as ecological changes increase in the locations where the species is distributed.