Abstract: Five representative sections including 16 samples of the spotted gums and its Corymbia relatives were selected as samples for genomic DNA extraction. PCR was performed using two pairs of primers. Target fragments for sequencing were derived from gel purification. Sequencing reaction was well improved and long fragment sequences were derived. Sequences were completely aligned and phylogenetic tree was reconstructed by using E. gunnii CCR as an outgroup. The results showed the percentage of A, C, G, and T of CCR in the 16 Corymbia samples were 24.92%,23.18%,23.22%and 28.67% respectively. The total of A+T (53.59%) was higher than that of G+C (46.41%). 292 variation sites (accounting for 9.71% in all analyzed sites), including 118 transitions, 97 transversions, and 93 indels (insertion/deletion), were found. Of the variation sites 185,accounting for 63.36% in total, were parsimonious informative sites. Some of the variation sites were overlapped. The ratio of transitions to transversions was 1.22:1.00. Phylogenetic tree of the 16 sample CCR gene indicated E. gunnii was a separate clade as an outgroup. All sections of Corymbia were resolved but Rufaria was strongly resolved. The Rufaria diverged earliest, followed by a weakly resolved Ochraria/Cadagaria clade. The Blakearia diverged next to the Politaria was the most recently evolved section. Multiple samples within the Politara provided the opportunity to test the resolution within the section.