We surveyed the natural distribution and current resource status of Erythrophleum fordii in South China. We investigated 11 phenotypic traits of fruits and seeds for 112 individuals in 8 natural populations to estimate variations within and among the populations and analyze relationships between phenotypic variation of these natural populations and their geographic and climate regimes. E. fordii was mainly distributed in the low-altitude areas near the Tropic of Cancer in Guangxi, Guangdong and Fujian Provinces and was generally scattered or naturally grew at a small scale because of heavy human disturbance. Length, width and morphological index of pods and seeds, quantity of seeds per pod, seed thickness, and weight per 1 000 seeds significantly differed within and among populations, and variations of pod traits within and among populations were all larger than those of seed traits. The quantity of seeds per pod showed a significant positive correlation with pod length, the morphological index of the pod, seed length and seed size, and seed length and width showed a positive correlation with pod size, as did weight per 1 000 seeds with pod width. The morphological index of pods showed a significant negative correlation with longitude. Positive correlations were seen between weight per 1 000 seeds and latitude; seed width and altitude and mean annual rainfall; morphological index of seeds and mean annual temperature; and seed size and mean annual rainfall. Hierarchical cluster analysis revealed these 8 populations divided into three groups: (1) GX03; (2) GX01 and GX02; and (3) GD01, GD02, GD03, GD04 and FJ01. These findings can offer basic data for further study of conservation biology and genetic breeding of this species.