The biodiversity are related to environmental status, the natural ponds contained more aquatic plant diversity than paddy field. Some species were found only in paddy fields e.g. Najas Graminea Del., while, some species were found only in natural water pond such as Ceratophyllum demersum Linn. Therefore these major species were selected for herbicide effect testing. The effect of glyphosate and butachlor on aquatic plant was observed in experiment, the color and morphology showed changing related to higher dose treatment. The RAPD profiles was analyzed for genomic template stability (GTS), the results indicated that GTS of Hydrilla verticellata was lowest (7.14%GTS), follow by Utricularia aurea lour (30.77 % GTS), Najas Graminea Del (38.71 %GTS), and Nitella sp. (59.38%GTS), respectively. The results indicated that these herbicides caused abnormally morphology and DNA instability, the RAPD profile cloud be used as biomarker for detection of herbicide contamination in aquatic ecological system.