Malania oleifera Chun et S.K. Lee is an endangered woody oil tree that produces nervonic acid, which is closely related to brain development. The phenotypic variation and diversity in some representative traits in natural populations are poorly understood. To investigate phenotypic variation, diversity and their relationship with geoclimatic factors, we evaluated 21 traits of 97 sampled individuals from seven natural populations. Coefficient of variation for 21 traits widely ranged from 0.05 (shape index of fruit) to 0.62 (water content of dry kernel), with an average of 0.18. The Shannon–Wiener indices ranged from 1.91 (water content of dry kernel) to 2.06 (leaf length and leaf width), with an average of 1.94. The variation of 20 traits was significantly influenced by the population effect (p < 0.05). The 21 traits were reduced to six principal components, which collectively accounted for 86.64% of the total phenotypic variation. The seven population was mainly divided into two groups: Group I, which included four populations distributed throughout the southern region and having wider and shorter leaves, larger fruit transverse diameters, and higher content of fatty acid and nervonic acid in the kernel, and Group II included the left populations with relative opposite characteristics to those in Group I. Trees with shorter leaves tend to produce oblate shape and heavier dried kernel, yielding more fatty acid and nervonic acids, and population-level pairwise kernel morphological distance were positively correlated with fatty acid distance (Mantel r = 0.39, p < 0.05). Annual average humidity was strongly positively correlated with leaf index (length/width, r = 0.78) but had a negative correlation with the kernel dry weight (r = −0.84). The shape of the kernel gradually altered from oblate to globose as longitude and rainfall increased. The environment became colder as latitude increased, resulting in a steady decrease in fatty acid content. No significant isolation by climatic and geographical distance was found for morphological and fatty acid variability. These results can have an important implication for genetic improvement, diversity conservation and resource management of the species in the future.

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