Tamarix chinensis Lour. is a shrub or 3-6-meter-tall small tree with high salt- and alkali- tolerance and aggressive invasiveness, mainly distributed in the eastern part of China in warm-temperate and subtropical climate zones. Molecular evidence indicated it expanded eastward from the western part of China quite recently in late Pleistocene about 0.02 Ma. With highly polymorphic microsatellites markers, we evaluated genetic structure and adaptation of nine T. chinensis populations mainly distributed in two estuarine flats of two climate zones: Yellow River Delta of warm-temperate and Hangzhou Bay of the subtropical zone. Despite a low population differentiation of FST= 0.0518, Bayesian clustering analysis, Discriminant Analysis of Principal Components (DAPC) and the unweighted pair group method with arithmetic mean (UPGMA) clearly identified three genetic clusters correlated to the populations’ geographic origin. Isolation by distance (IBD) and isolation by environment (IBE) patterns were detected at significant levels. A series of redundancy analyses (RDA) revealed significant contributions of geographical and environmental factors to genetic variation measured with environmental factors explaining a larger variance. The FST-based test (BayeScan) determined 5 out of 8 SSRs as outlier loci possibly at balancing selection. Further landscape genetic analysis identified some alleles significantly correlated to environmental variables including maximum temperature of the warmest month, minimum temperature of coldest month, and isothermality, signaling the adaptation of T. chinensis to temperature in two climate zones. Our result showed rapid evolution happened at a small temporal scale in a woody species with short generation time.