【Objective】 Genomic loci that are significantly associated with population adaptation were detected inEucalyptus cloeziana F. Muell. populations to obtain useful molecular information for germplasm conservation and utilization. 【Method】 Seven northern and southern populations of E. cloeziana were analyzed using 84 simple sequence repeats (SSR) markers [29 genomic SSRs and 55 expressed sequence tag (EST) derived SSRs]. Isolation by distance (IBD) among populations was determined using Mantel test. Outlier loci ofF-statistics of between-population differentiation (F_st) and their significant allelic associations with habitat climatic variables were investigated for all the SSR loci, with further functional annotation of the significantly associated loci against the NCBI non-redundant protein database. 【Result】 IBD was revealed between the northern and southern populations of E.cloeziana, and the clustering analysis based on 19 climatic variables also resulted in division of the northern and southern populations into independent groups, suggesting the climatic effect on driving the population divergence. A total of 39 F_st outliers (46.4%) were identified as selective loci. Specifically, the software LOSITAN detected 12 positive and 17 balancing selection loci. Six alleles from five outlier loci were identified with spatial analysis methods, each associated significantly with one or more climatic factors (P < 0.001) and showed dramatic difference in allelic frequency between the northern and southern populations. Among the six significant alleles, Embra6-118 bp was associated with the minimum temperature of the coldest month ( T_mcm), with the locus Embra6 functionally annotated as basic helix-loop-helix (bHLH) transcript factor bHLH155. The allele Embra20-121 bp was associated with the precipitation of the warmest quarter (P_wq), with Embra20 functionally annotated as sucrose transporters. EUCeSSR676-168 bp was associated with T_mcm, P_wq, the mean annual temperature (T_ma) and the minimum temperature of the warmest month (T_mwm), with the locus functionally annotated as photosystem II stability/assembly factor HCF136. However, the two other significant markers EUCeSSR298 and EUCeSSR1009 were of unknown function. 【Conclusion】 The divergence between the northern and southern populations of E. cloeziana was strongly related with historical climate, and there might be glacial refugia in the northern and southern zones during the Quaternary. The marked difference in the frequency of climate-associated SSR alleles between the northern and southern populations provides molecular evidence for positive selection oriented climatic adaptation in E. cloeziana.