To clarify the phenotypic variation， genetic diversity， and population genetic structure of natural populations of Michelia macclurei in southeastern Guangxi， and to identify SSR markers associated with important phenotypic traits， this study used 120 superior tree resources collected from five natural populations in southeastern Guangxi as experimental materials. Thirteen phenotypic traits were measured， and genotyping was performed using 10 SSR primer pairs. Cluster analysis， population structure analysis， and a mixed linear model （MLM） were employed to evaluate genetic diversity and marker-trait associations. The results showed significant differences among the five populations in leaf morphological and physiological and biochemical traits. Among them， the BL population exhibited larger leaves and higher biomass， whereas the CW population showed significantly higher average malondialdehyde and free proline contents. The YL and LW populations showed the smallest phenotypic distance. A total of 77 alleles were detected using the 10 SSR primer pairs， with an average number of alleles of 7.70 and an average effective number of alleles of 3.72. The mean observed heterozygosity and expected heterozygosity were 0.53 and 0.66， respectively， and the mean polymorphism information content was 0.62. Among the five populations， the YL population showed the highest genetic diversity， whereas the high-altitude LW population showed the lowest. The average genetic differentiation coefficient among populations was 0.11， and average gene flow was 2.89. Genetic structure analysis indicated that the BL and YL populations retained relatively independent genetic components， whereas the remaining populations showed obvious genetic admixture. Association analysis detected six SSR loci significantly associated with phenotypic traits， with phenotypic variation explained ranging from 6.87% to 18.90%. Among them， locus M23 was significantly associated with multiple traits. This study revealed the genetic variation of M. macclurei in southeastern Guangxi， and the associated loci identified here can provide a theoretical basis for germplasm resources conservation， elite germplasm resources screening， and marker-assisted breeding of M. macclurei.