In the present study, the variation partitioning technique was applied to investigate the influence of space and environment on the variation in haplotype composition of different populations of Chrysanthemum indicum L. (Compositae) in China. Species niche modeling was employed as well to predict and map the suitable area of C. indicum in China. Through variation partitioning, the results showed that, environment solely could not explain any percent of the variation in haplotype composition, while space on its own could explain around 12.2% of the total variation in haplotype composition. Finally, the interaction between environment and space explained additional 11.1% of the total variation. As such, geographic distance is the only driver of haplotype diversity among different populations of C. indicum. Modeling speciesï¿½ suitable ranges indicated that most central and eastern parts of China have higher occurrence probabilities of the species. The most influential predictors contributing to the distributional modeling were annual minimum temperature, annual maximum temperature and annual humidity. However, given that up to 75% of the total variation in hyplotype structure is unexplained, further sampling of different populations at distinct habitats is required so as to better quantify the relative influence of environment and space on the genetic structure of C. indicum populations.