Understanding the genetic variability of hybrids provides information on their current and future evolutionary role. In this paper, we focus on the interspecific hybridRanunculus circinatus×R. fluitansthat forms spontaneously within the groupRanuculusL. sect.BatrachiumDC. (Ranunculaceae Juss.). Genome-wide DNA fingerprinting using amplified fragment length polymorphisms (AFLP) was employed to determine the genetic variation among 36 riverine populations of the hybrid and their parental species. The results demonstrate a strong genetic structure ofR. circinatus×R. fluitanswithin Poland (Central Europe), which is attributed to independent hybridization events, sterility of hybrid individuals, vegetative propagation, and isolation through geographical distance within populations. The hybridR. circinatus×R. fluitansis a sterile triploid, but, as we have shown in this study, it may participate in subsequent hybridization events, resulting in a ploidy change that can lead to spontaneous fertility recovery. The ability to produce unreduced female gametes of the hybridR. circinatus×R. fluitansand the parental speciesR. fluitansis an important evolutionary mechanism inRanunculussect.Batrachiumthat could give rise to new taxa.