The objective of this study is to elucidate the efficiency of enation-structure (at node) recognition method at pre-flowing stage and to understand the population genetic variation of the Mikania weeds in Taiwan. The plant materials collected by recognizing enation-structure symptom method from North, Central, South and East Taiwan and off-shore islands. Using PCR¡V sequencing marker techniques, the sequencing revealed that nrDNA ITS region could identify three Mikania weeds and the 97% similarity of phylogenetic relationship between M.cordata and M.micrantha are more closer than that between M.cordata and M.scandens, whose ITS sequence is obtained from GeneBank. However ,the sequences of chloroplast DNA of M.cordata and M.micrantha at trnL intron¡]436bp¡^or trnL-trnF IGS¡]345 bp¡^are almost the same and could not be used as molecular markers. The recognizing techniques of enation-structure was supported by the nrDNA ITS region and ISSR results at the end, thus the finding can be recommended to the Council of Agriculture in order to eliminate the weed and to reduce the impact on M.cordata, which is native in Taiwan. Moreover, the findings of ISSR analysis in the aspect of population genetic variation indicated that high genetic differentiation ¡]Gst>0.5¡^was found among the M. cordata and M.micrantha populations. Based on the Mantle test, there was no relationship between genetic distance and geographic distance in M.micrantha¡]r=0.0053,p=0.47¡^.This phenomenon revealed that populations of M.micrantha had complex population variability within the short-term invaded into Taiwan that might be resulted from the random dispersion of human activities. The population of M.micrantha was established by few individuals (founders) and grown rapidly in Taiwan, resulting in population differentiation via genetic drift. In contrast to M.micrantha ,there was relationship between genetic distance and geographic distance in M.cordata ¡]r=0.44,p=0.025¡¯¡^.It revealed that populations of M.cordata agreed to the concept of isolation by distance model, which might be evolved from the result of natural dispersion. In conclusion, the population structure of M.micrantha in Taiwan is stable , suggesting that control of Mikania population should be based on different populations where have large differentiation among them .