By using litterbag method, this paper studied the decomposition of the leaf- and flower litters of two emergent macrophytes, native species Phragmites australis and invasive species Spartina alterniflora, and related affecting factors in the Minjiang River estuary of East China. In the decomposition process of the litters, the decay of standing litter (0-90 days) was an important period, and the loss rate of the flower- and leaf litters dry mass of P. australis and S. alterniflora was 15.0 +/- 3.5% and 13.3 +/- 1.1%, and 31.9 +/- 1.1% and 20.8 +/- 1.4%, respectively. During lodging decay period (91-210 days), the loss rate of the flower- and leaf litters dry mass of P. australis and S. alterniflora was 69.5 +/- 0.6% and 71.5 +/- 2.5%, and 76.8 +/- 1.9% and 67.5 +/- 2.1%, respectively. In standing decay period, the decomposition rate of the two plants litters was positively correlated with the litters C/N but negatively correlated to the litters N/P, and the litters P was an important factor limiting the litters decay. In lodging decay period, the effects of the litters C/N, C/P, and N/P decreased, while the environment factors (climate, soil moisture, soil acidity and salinity, and sediment properties) acted more important roles. The differences in the factors affecting the decay of the litters in different decomposition periods were mainly related to the micro-environment and tidal process for the two plant communities.