The versatile rhizomatous terrestrial form of the perennial weed Persicaria amphibia is reported to cause severe infestations in potato crops, which are mainly cultivated as a monoculture in the area of Kato Nevrokopi located at the Greek-Bulgarian boundaries. This weed cannot be easily eradicated from potato crops in Northern Greece and therefore, the accurate taxonomic identification of P. amphibia has a high economical importance. The generic classification of P. amphibia has been unstable, mostly due to different morphological interpretations with other Persicaria species. Molecular studies based on DNA sequence data from the rbcL and matK plastid regions supported 100% homology with P. amphibia. Further analysis using the psbK-psbI, atpF-atpH, rpoC1 and rpoB plastid regions identified distinct differences with other Persicaria species suggesting the application of psbK-psbI and atpF-atpH as potential molecular markers for identification and phylogenetic analysis of Persicaria taxa. Morphology description and ecology characteristics concerning the terrestrial form of P. amphibia are provided. A multidisciplinary approach with both molecular and morphological information is described in this study and provides potential useful tools for the identification and taxonomy of Persicaria species. © Biotechnol. & Biotechnol.