The changes of ultrastructure under scanning electron microscopy and transmission electron microscopy were described in two duckweed species of Lenma aequinoctialis and Spirodela polyrrihza cultivated in ammonia medium in present study,contrasted by the ones growing under nitrate medium.The result showed that outstanding cell wall in lower epidermis became crinkly and disappeared partly in fronds under ammonia medium.The stomata on the upper epidermis opened much wider far more than ones under nitrate medium.The chloroplast membrane limiting became blurred and disappeared partly in fronds under ammonia medium.The whole chloroplast of fronds under ammonia medium presented the trending of disassembly.And the internal membrane network including grana lamellae and stroma lamellae break off.In contrast to ones under nitrate medium,more starch grain appeared amongst stroma.Based on the results of observation,the toxicity mechanism of un-ionized ammonia(NH_3) and ammonium ion(NH~+_4) to duckweed were respectively discussed.