Eucalyptus cloeziana is a valuable timber tree species for its high durability and excellent sawmilling qualities. However, there is lack of complete genomic information for this plant, which severely constrains its genetic improvement. This study aim to survey the genome of E. cloeziana and determine the large-scale sequencing scheme of this species. Next-generation sequencing based on Illumina Hi-Seq X Ten platform was used to survey the E. cloeziana genome and its SSR markers development. We estimated the genome size to be 491.91 Mb and the heterozygosity rate to be 1.23%, with repetitive sequences accounting for 40.74%. The clean reads of E. cloeziana were assembled into 995,093 scaffolds (556,992,952 bp) with a N50 value of 2297 bp. In the GO database, the 10,172 genes annotated were matched to 50 functional gene groups in three categories of cell component, biological function and molecular function, respectively. Through KEGG pathways analysis, 10,802 genes were successfully annotated and 133 metabolic pathways were detected with the most abundant metabolism-related genes. Meanwhile, a total of 58,832 simple-sequence repeat (SSR) loci were identified in the E. cloeziana genome, and among them, dinucleotide repeats were the most abundant class. AG/CT, AT/AT, AAG/CTT were the three most frequent primitive types. Of the 50 genomic SSR primer pairs randomly selected for screening test, 13 showed polymorphism (PIC = 0.625). Three to nine alleles per locus (mean = 6.23) were observed, with the observed and expected heterozygosity at 0.317–1.000 and 0.276–0.838across all the 44 E. cloeziana germplasms, respectively. Here, we report the genome information of E. cloeziana, and the novel 13 genomic SSR markers that were developed can be used as powerful tools for evaluating genetic diversity and population structure, and thus contribute to molecular breeding studies of E. cloeziana and other eucalypts.