A precise and selective reversed phase high-performance liquid chromatographic method (HPLC) was used to quantify the levels of huperzine A in samples of three Huperzia serrata populations with a total of 73 individuals located in Zhejiang, Guangxi, Chongqing, respectively, as well as in one-to-one samples of these 73 individuals introduced in same site after one year. Huperzine A content variation both among and within populations, and the dynamic change of this alkaloid occurring in same population after one year introduction, were analyzed using SPSS 13.0 software (Coefficient of variation, One-way ANOVA analysis, Paired-samples T tests). The results indicated that huperzine A content varied significantly by geographical locations, especially change with longitude, i. e., the order of the huperzine A content was CQ population > GX population > ZJ population. The coefficients of variation (CV) were as follows: 0.36 (CQ), 0.44 (GX) and 0.40 (ZJ). This indicated that there was plentiful diversity concerned with huperzine A content among individuals within population. Moreover, this high diversity was still maintained after one year introduction. ANOVA analysis showed that there was significant difference among populations in huperzine A content. Finally, the significant change of huperzine A content was not observed in all three populations after one year introduction. The results presented in this study could provide evidence that the huperzine A content variation of H. serrata is the results of an interaction between genes and the environment, by comparison, is mainly controlled by genetic factor.