A first assessment of genetic diversity and expansion of the invasive species Amorpha fruticosa L. was estimated in the 91E0* (Annex I Dir. 92/43/EEC) priority habitat of Nestos. A. fruticosa is a perennial deciduous shrub belonging to the family Fabaceae and is native to the south-western part of North America, which recently was introduced to Europe as an ornamental plant. Its expansion through the cross-border river of Nestos has significant negative effects on the 91E0* habitat (a habitat with Alnus glutinosa, Populus alba, and Ulmus minor). Herein, we studied the genetic diversity with amplified fragment length polymorphisms fragments of eastern and western populations in order to see if there is one genetic pool for the species. Furthermore, we estimated the regeneration index (IR) in order to see the potential expansion of this invasive species. Results showed that eastern and western populations have almost equal heterozygosity (He) and with a slightly higher value for the western population, which was in agreement with the results of the IR. This is an innovative study that discusses the implications of A. fruticosa of 91E0* habitat in Nestos and proposes management measures to eliminate its expansion and improve the resilience of the habitat.