To reveal the genetic diversity of naturalized Narcissus tazetta var. chinensis populations in eastern coast of China, 49 individuals from five representative populations distributed in Shanghai, Zhejiang and Fujian Proviences were evaluated by using two chloroplast DNA matK and trnH-psbA fragments. The results showed that total of six haplotypes were identified from the combined two sequences with an alignment length of 1 443 bp. The genetic diversity of naturalized population was in order of DLSY > PTD > NJD=ZZ > CMD. AMOVA analysis showed that the variation within populations was the main source of the genetic variation (91.98%) and low genetic differentiation between populations (Fst=0.080 22). Insignificant phylogeographic structure was detected at species level (Nst=0.020 < Gst=0.031; P<0.05). Mantel test showed a significant linear correlation between genetic distance and geographical distance (r=0.929, P=0.02<0.05). The neutrality test combined bimodal curve in mismatch distribution analysis both rejected the hypothesis of the demographic expansion of these populations. Analysis of median network and phylogenetic NJ tree based on the distribution of haplotype both divided all the populations into two major branches. These indicated a low level of genetic diversity with a weak genetic differentiation among Narcissus tazetta var. chinensis populations in eastern coast of China. Genetic variation mainly occurs in populations, while species had experienced no demographic expansion. These might likely owing to the gene flows which were caused by the combination of islands segregation, biological characteristics, habitat heterogeneity as well as human disturbance.