An increasing number of invasive organisms are responsible for adverse environmental and economic impacts worldwide, including species extinction, crop failures, reduced water supply, and damage to industrial infrastructures. Many invasive plants are horticultural or agronomic crops that have escaped cultivation. Invasive species control is costly and continues to escalate due to new crop domestication and increased international trade. The purpose of presented research was to characterize the invasive potential of select Czech and US (Minnesota) native and introduced reed canary grass (Phalaris arundinacea) genotypes, to asses the invasive potential of P. arundinacea native/invasive/expansive populations and cultivars, and to reveal level of genetic polymorphism within and between populations and cultivars of P.arundinacea in geographical gradient and to asses gene-flow between populations. Reed canary grass germplasm in both Minnesota (MN) and the Czech Republic (CR) was collected and assessed for genetic variation using molecular techniques. Other morphological (phenotypic), domestication, and biochemical traits were also studied. The fast evolving microsatellites (ISSRs) were used as the fingerprinting marker. A set of at three ISSR markers (UBC810, UBC828 a UBC881) was analysed. Results showed unusually high degree of variability in the analyzed samples. Individual populations were very heterogeneous and hypothesis that Phalaris creates large monoclonal stands was not supported. Also intrapopulation variability was very high and it was not entirely clear differentiation between CZ populations. In contrast, within a large geographic scale significant differentiation was demonstrated between the U.S. and CZ populations. This study was supported by grants MSM60076658-06, GAJU 064/2010/Z, AMVIS LH11-039.