<p><i>Camellia reticulata</i> Lindl., an endemic polyploid complex in southwestern China, has considerable ornamental value and great potential for edible oil production. However, its natural populations have declined dramatically due to illegal poaching for horticultural trade and anthropogenic habitat destruction. Therefore, evaluating the genetic diversity and population structure of <i>C. reticulata</i> is imperative for the conservation of its genetic resources and the development of its breeding strategies. This study developed 22 SSR loci and applied them to assess the genetic diversity of 292 <i>C. reticulata</i> individuals from eight natural populations. These loci detected 434 alleles, with a mean of 19.727 alleles per locus (<i>N</i>a). The expected heterozygosity (<i>H</i>e), polymorphic information content (<i>PIC</i>), and Shannon’s information index (<i>I</i>) were 0.828, 0.811, and 2.132 at the species level, and were 0.773, 0.746 and 1.805 at the population level, respectively, indicating a high level of genetic diversity in <i>C. reticulata</i>. Analysis of molecular variance showed that most genetic variation (81.27%) existed within populations. Bayesian clustering classified the eight populations into two distinct clusters. The high genetic diversity of <i>C. reticulata</i> may be attributed to polyploidization and habitat heterogeneity across its natural ranges.</p>