The genetic diversity and genetic structure of 4 wild seedling populations of Rhododendron molle (64 individuals) from 3 provinces were analyzed with 20 pairs of polymorphic simple sequence repeat (SSR) primers developed by our group. We aim to provide some theoretical basis for the conservation of R. molle. The results showed: (1) 314 alleles were amplified by 20 pairs of SSR primers, the average number of alleles of each SSR site was 15.700, and the mean values of polymorphic information content (PIC) and the effective alleles number (N_e) were 0.850 and 4.457, respectively. (2) The mean value of the genetic diversity index (H) and Shannon diversity index (I) of the seedling population of R. molle were 0.717 and 1.557, respectively. The genetic diversity of Jinxi (Jiangxi Province) population exhibits great level of variability, whereas the population of Panan (Zhejiang Province) exhibits the lowest level of variability. (3) Based on the analysis of the infinite allele model (IAM), it was found that the gene flow (N_m) and the genetic differentiation coefficient (F_st) of the seedling population of R. molle (F_st) were 1.372 and 0.155, respectively. AMOVA analysis showed that the probability of variation of the seedling population of R. molle mainly occurred in the middle population (86.0%), and the interpopulation variation was only 14%; (4) The results of neighbor joining (NJ) analysis and structure classification were basically similar, which are divided into 3 and 4 groups, respectively. Comprehensive comparative analysis found that the index parameters related to the genetic diversity of the seedling population of R. molle were all lower than the natural population of adults, which indicated that the fragmentation of habitat had posed a great threat to the survival of R. molle.